--- emboss-6.4.0.orig/debian/emboss.install
+++ emboss-6.4.0/debian/emboss.install
@@ -0,0 +1,2 @@
+debian/emboss_tmp/usr/lib usr
+#debian/abiview.desktop usr/share/applications
--- emboss-6.4.0.orig/debian/emboss-doc.doc-base.emboss-groups
+++ emboss-6.4.0/debian/emboss-doc.doc-base.emboss-groups
@@ -0,0 +1,9 @@
+Document: emboss-groups
+Title: EMBOSS Application Groups
+Author: The EMBOSS Developpers
+Section: Science/Biology
+Abstract: Documentation of the EMBOSS applications organized into logical groups according to their function.  
+
+Format: HTML
+Index: /usr/share/doc/emboss-doc/doc/programs/html/groups.html
+Files: /usr/share/doc/emboss-doc/doc/programs/html/*.html
--- emboss-6.4.0.orig/debian/watch
+++ emboss-6.4.0/debian/watch
@@ -0,0 +1,2 @@
+version=3
+ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-([\d.]*)\.tar\.gz
--- emboss-6.4.0.orig/debian/emboss.docs
+++ emboss-6.4.0/debian/emboss.docs
@@ -0,0 +1,7 @@
+AUTHORS
+FAQ
+NEWS
+KNOWN_BUGS
+PROBLEMS
+THANKS
+debian/reference 
--- emboss-6.4.0.orig/debian/emboss.manpages
+++ emboss-6.4.0/debian/emboss.manpages
@@ -0,0 +1,316 @@
+debian/manpages/aaindexextract.1e
+debian/manpages/abiview.1e
+debian/manpages/acdc.1e
+debian/manpages/acdlog.1e
+debian/manpages/acdpretty.1e
+debian/manpages/acdrelations.1e
+debian/manpages/acdtable.1e
+debian/manpages/acdtrace.1e
+debian/manpages/acdvalid.1e
+debian/manpages/ajbad.1e
+debian/manpages/ajfeatest.1e
+debian/manpages/ajtest.1e
+debian/manpages/aligncopy.1e
+debian/manpages/aligncopypair.1e
+debian/manpages/antigenic.1e
+debian/manpages/backtranambig.1e
+debian/manpages/backtranseq.1e
+debian/manpages/banana.1e
+debian/manpages/biosed.1e
+debian/manpages/btwisted.1e
+debian/manpages/cachedas.1e
+debian/manpages/cachedbfetch.1e
+debian/manpages/cacheebeyesearch.1e
+debian/manpages/cacheensembl.1e
+debian/manpages/cai.1e
+debian/manpages/chaos.1e
+debian/manpages/charge.1e
+debian/manpages/checktrans.1e
+debian/manpages/chips.1e
+debian/manpages/cirdna.1e
+debian/manpages/codcmp.1e
+debian/manpages/codcopy.1e
+debian/manpages/coderet.1e
+debian/manpages/complex.1e
+debian/manpages/compseq.1e
+debian/manpages/cons.1e
+debian/manpages/consambig.1e
+debian/manpages/corbatest.1e
+debian/manpages/cpgplot.1e
+debian/manpages/cpgreport.1e
+debian/manpages/cusp.1e
+debian/manpages/cutgextract.1e
+debian/manpages/cutseq.1e
+debian/manpages/dan.1e
+debian/manpages/dastest.1e
+debian/manpages/dbfetchtest.1e
+debian/manpages/dbget.1e
+debian/manpages/dbgeturl.1e
+debian/manpages/dbiblast.1e
+debian/manpages/dbifasta.1e
+debian/manpages/dbiflat.1e
+debian/manpages/dbigcg.1e
+debian/manpages/dbshowdat.1e
+debian/manpages/dbshowquery.1e
+debian/manpages/dbtell.1e
+debian/manpages/dbtellquery.1e
+debian/manpages/dbxcompress.1e
+debian/manpages/dbxedam.1e
+debian/manpages/dbxfasta.1e
+debian/manpages/dbxflat.1e
+debian/manpages/dbxgcg.1e
+debian/manpages/dbxobo.1e
+debian/manpages/dbxreport.1e
+debian/manpages/dbxresource.1e
+debian/manpages/dbxstat.1e
+debian/manpages/dbxtax.1e
+debian/manpages/dbxuncompress.1e
+debian/manpages/degapseq.1e
+debian/manpages/density.1e
+debian/manpages/descseq.1e
+debian/manpages/diffseq.1e
+debian/manpages/digest.1e
+debian/manpages/distmat.1e
+debian/manpages/docxmlvalid.1e
+debian/manpages/docxmlwell.1e
+debian/manpages/domtesta.1e
+debian/manpages/domtestb.1e
+debian/manpages/domtestc.1e
+debian/manpages/domtestd.1e
+debian/manpages/dotmatcher.1e
+debian/manpages/dotpath.1e
+debian/manpages/dottup.1e
+debian/manpages/dreg.1e
+debian/manpages/drfinddata.1e
+debian/manpages/drfindformat.1e
+debian/manpages/drfindid.1e
+debian/manpages/drfindresource.1e
+debian/manpages/drget.1e
+debian/manpages/drtext.1e
+debian/manpages/edamclean.1e
+debian/manpages/edamdef.1e
+debian/manpages/edamhasinput.1e
+debian/manpages/edamhasoutput.1e
+debian/manpages/edamisformat.1e
+debian/manpages/edamisid.1e
+debian/manpages/edamname.1e
+debian/manpages/edialign.1e
+debian/manpages/einverted.1e
+debian/manpages/embossdata.1e
+debian/manpages/embossversion.1e
+debian/manpages/emma.1e
+debian/manpages/emowse.1e
+debian/manpages/ensembltest.1e
+debian/manpages/entrails.1e
+debian/manpages/entrailsbook.1e
+debian/manpages/entrailshtml.1e
+debian/manpages/entrailswiki.1e
+debian/manpages/entret.1e
+debian/manpages/entrygo.1e
+debian/manpages/entrytax.1e
+debian/manpages/epestfind.1e
+debian/manpages/eprimer32.1e
+debian/manpages/eprimer3.1e
+debian/manpages/equicktandem.1e
+debian/manpages/est2genome.1e
+debian/manpages/etandem.1e
+debian/manpages/extractalign.1e
+debian/manpages/extractfeat.1e
+debian/manpages/extractseq.1e
+debian/manpages/featcopy.1e
+debian/manpages/featreport.1e
+debian/manpages/feattext.1e
+debian/manpages/findkm.1e
+debian/manpages/freak.1e
+debian/manpages/fuzznuc.1e
+debian/manpages/fuzzpro.1e
+debian/manpages/fuzztran.1e
+debian/manpages/garnier.1e
+debian/manpages/geecee.1e
+debian/manpages/getorf.1e
+debian/manpages/godef.1e
+debian/manpages/goname.1e
+debian/manpages/goseq.1e
+debian/manpages/helixturnhelix.1e
+debian/manpages/histogramtest.1e
+debian/manpages/hmoment.1e
+debian/manpages/idtell.1e
+debian/manpages/iep.1e
+debian/manpages/infoalign.1e
+debian/manpages/infobase.1e
+debian/manpages/inforesidue.1e
+debian/manpages/infoseq.1e
+debian/manpages/intconv.1e
+debian/manpages/isdbdata.1e
+debian/manpages/isdbname.1e
+debian/manpages/isochore.1e
+debian/manpages/jaspextract.1e
+debian/manpages/jaspscan.1e
+debian/manpages/lindna.1e
+debian/manpages/listor.1e
+debian/manpages/makenucseq.1e
+debian/manpages/makeprotseq.1e
+debian/manpages/marscan.1e
+debian/manpages/martattributes.1e
+debian/manpages/martdatasets.1e
+debian/manpages/martfilters.1e
+debian/manpages/martquery.1e
+debian/manpages/martregistry.1e
+debian/manpages/martseqs.1e
+debian/manpages/maskambignuc.1e
+debian/manpages/maskambigprot.1e
+debian/manpages/maskfeat.1e
+debian/manpages/maskseq.1e
+debian/manpages/matcher.1e
+debian/manpages/megamerger.1e
+debian/manpages/merger.1e
+debian/manpages/msbar.1e
+debian/manpages/mwcontam.1e
+debian/manpages/mwfilter.1e
+debian/manpages/needle.1e
+debian/manpages/needleall.1e
+debian/manpages/newcoils.1e
+debian/manpages/newcpgreport.1e
+debian/manpages/newcpgseek.1e
+debian/manpages/newseq.1e
+debian/manpages/nohtml.1e
+debian/manpages/noreturn.1e
+debian/manpages/nospace.1e
+debian/manpages/notab.1e
+debian/manpages/notseq.1e
+debian/manpages/nthseq.1e
+debian/manpages/nthseqset.1e
+debian/manpages/octanol.1e
+debian/manpages/oddcomp.1e
+debian/manpages/ontocount.1e
+debian/manpages/ontoget.1e
+debian/manpages/ontogetcommon.1e
+debian/manpages/ontogetdown.1e
+debian/manpages/ontogetobsolete.1e
+debian/manpages/ontogetroot.1e
+debian/manpages/ontogetsibs.1e
+debian/manpages/ontogetup.1e
+debian/manpages/ontoisobsolete.1e
+debian/manpages/ontotext.1e
+debian/manpages/origsplitter.1e
+debian/manpages/origunion.1e
+debian/manpages/palindrome.1e
+debian/manpages/pasteseq.1e
+debian/manpages/patmatdb.1e
+debian/manpages/patmatmotifs.1e
+debian/manpages/patmattest.1e
+debian/manpages/pepcoil.1e
+debian/manpages/pepdigest.1e
+debian/manpages/pepinfo.1e
+debian/manpages/pepnet.1e
+debian/manpages/pepstats.1e
+debian/manpages/pepwheel.1e
+debian/manpages/pepwindow.1e
+debian/manpages/pepwindowall.1e
+debian/manpages/plotcon.1e
+debian/manpages/plotorf.1e
+debian/manpages/polydot.1e
+debian/manpages/preg.1e
+debian/manpages/prettyplot.1e
+debian/manpages/prettyseq.1e
+debian/manpages/prima.1e
+debian/manpages/primers.1e
+debian/manpages/primersearch.1e
+debian/manpages/printsextract.1e
+debian/manpages/profit.1e
+debian/manpages/prophecy.1e
+debian/manpages/prophet.1e
+debian/manpages/prosextract.1e
+debian/manpages/pscan.1e
+debian/manpages/psiphi.1e
+debian/manpages/rebaseextract.1e
+debian/manpages/recoder.1e
+debian/manpages/redata.1e
+debian/manpages/remap.1e
+debian/manpages/restover.1e
+debian/manpages/restrict.1e
+debian/manpages/revseq.1e
+debian/manpages/seealso.1e
+debian/manpages/seqcount.1e
+debian/manpages/seqgo.1e
+debian/manpages/seqinfo.1e
+debian/manpages/seqmatchall.1e
+debian/manpages/seqret.1e
+debian/manpages/seqretall.1e
+debian/manpages/seqretallfeat.1e
+debian/manpages/seqretset.1e
+debian/manpages/seqretsetall.1e
+debian/manpages/seqretsingle.1e
+debian/manpages/seqretsplit.1e
+debian/manpages/seqrettype.1e
+debian/manpages/seqtax.1e
+debian/manpages/seqxref.1e
+debian/manpages/seqxrefall.1e
+debian/manpages/seqxrefget.1e
+debian/manpages/servertell.1e
+debian/manpages/showalign.1e
+debian/manpages/showdb.1e
+debian/manpages/showfeat.1e
+debian/manpages/showorf.1e
+debian/manpages/showpep.1e
+debian/manpages/showseq.1e
+debian/manpages/showserver.1e
+debian/manpages/shuffleseq.1e
+debian/manpages/sigcleave.1e
+debian/manpages/silent.1e
+debian/manpages/sirna.1e
+debian/manpages/sixpack.1e
+debian/manpages/sizeseq.1e
+debian/manpages/skipredundant.1e
+debian/manpages/skipseq.1e
+debian/manpages/splitsource.1e
+debian/manpages/splitter.1e
+debian/manpages/sqltest.1e
+debian/manpages/stretcher.1e
+debian/manpages/stssearch.1e
+debian/manpages/supermatcher.1e
+debian/manpages/syco.1e
+debian/manpages/taxget.1e
+debian/manpages/taxgetdown.1e
+debian/manpages/taxgetrank.1e
+debian/manpages/taxgetspecies.1e
+debian/manpages/taxgetup.1e
+debian/manpages/taxseq.1e
+debian/manpages/tcode.1e
+debian/manpages/testplot.1e
+debian/manpages/textget.1e
+debian/manpages/textsearch.1e
+debian/manpages/texttotext.1e
+debian/manpages/texttoxml.1e
+debian/manpages/textvalid.1e
+debian/manpages/tfextract.1e
+debian/manpages/tfm.1e
+debian/manpages/tfscan.1e
+debian/manpages/tmap.1e
+debian/manpages/tranalign.1e
+debian/manpages/transeq.1e
+debian/manpages/treetypedisplay.1e
+debian/manpages/trimest.1e
+debian/manpages/trimseq.1e
+debian/manpages/trimspace.1e
+debian/manpages/twofeat.1e
+debian/manpages/union.1e
+debian/manpages/urlget.1e
+debian/manpages/vectorstrip.1e
+debian/manpages/water.1e
+debian/manpages/whichdb.1e
+debian/manpages/wobble.1e
+debian/manpages/wordcount.1e
+debian/manpages/wordfinder.1e
+debian/manpages/wordmatch.1e
+debian/manpages/wossdata.1e
+debian/manpages/wossinput.1e
+debian/manpages/wossname.1e
+debian/manpages/wossoperation.1e
+debian/manpages/wossoutput.1e
+debian/manpages/wossparam.1e
+debian/manpages/wosstopic.1e
+debian/manpages/xmltotext.1e
+debian/manpages/xmltoxml.1e
+debian/manpages/xmltransform.1e
+debian/manpages/yank.1e
--- emboss-6.4.0.orig/debian/abiview.desktop
+++ emboss-6.4.0/debian/abiview.desktop
@@ -0,0 +1,16 @@
+[Desktop Entry]
+Version=1.0
+Terminal=false
+#Icon=abiview
+Exec=abiview -outseq /dev/null -graph x11 %f
+Name=abiview
+GenericName=Chromatogram viewer
+GenericName[en]=Chromatogram viewer
+GenericName[fr]=Visualisateur de chromatogrammes
+Comment=Displays ABIF Applied Biosystems Inc. chromatograms. 
+Comment[en]=Displays ABIF Applied Biosystems Inc. chromatograms. 
+Comment[fr]=Affiche les chromatogrammes au format ABIF (Applied Biosystems Inc.).
+Type=Application
+Categories=Biology;Science;Education;
+MimeType=application/vnd.appliedbiosystems.abif;
+NoDisplay=true
--- emboss-6.4.0.orig/debian/build-manpages.sh
+++ emboss-6.4.0/debian/build-manpages.sh
@@ -0,0 +1,16 @@
+#!/bin/sh -e
+# Copyleft 2007 Charles Plessy, do what you want with this trivial file.
+
+PACKAGE=$(dpkg-parsechangelog -ldebian/changelog | grep Source: | cut -f2 -d' ')
+VERSION=$(dpkg-parsechangelog -ldebian/changelog | grep Version: | cut -f2 -d' ' | cut -f1 -d-)
+ORIGTARGZ=../${PACKAGE}_${VERSION}.orig.tar.gz
+
+rm -f debian/$PACKAGE.manpages
+
+for FILE in $(ls emboss/acd/*.acd)
+  do
+  ACD=$(basename $FILE .acd)
+  ./debian/acd2docbook.pl $FILE ${VERSION} \
+  | xsltproc --nonet --param man.charmap.use.subset 0 -o debian/manpages/ -
+  echo "debian/manpages/$ACD.1e" >> debian/$PACKAGE.manpages
+done
--- emboss-6.4.0.orig/debian/emboss.mime
+++ emboss-6.4.0/debian/emboss.mime
@@ -0,0 +1,6 @@
+application/vnd.appliedbiosystems.abif; abiview -auto '%s' ; description=ABIF Applied Biosystems Inc. chromatogram; nametemplate=%s.ab1
+application/x-dna; abiview -auto '%s' ; description=ABIF Applied Biosystems Inc. chromatogram; nametemplate=%s.ab1
+application/abi1; abiview -auto '%s' ; description=ABIF Applied Biosystems Inc. chromatogram; nametemplate=%s.ab1
+application/vnd.appliedbiosystems.abif; seqret -filter '%s' ; description=ABIF Applied Biosystems Inc. chromatogram; nametemplate=%s.ab1 ; copiousoutput
+application/x-dna; seqret -filter '%s' ; description=ABIF Applied Biosystems Inc. chromatogram; nametemplate=%s.ab1 ; copiousoutput
+application/abi1; seqret -filter '%s' ; description=ABIF Applied Biosystems Inc. chromatogram; nametemplate=%s.ab1 ; copiousoutput
--- emboss-6.4.0.orig/debian/compat
+++ emboss-6.4.0/debian/compat
@@ -0,0 +1 @@
+9
--- emboss-6.4.0.orig/debian/jemboss.desktop
+++ emboss-6.4.0/debian/jemboss.desktop
@@ -0,0 +1,10 @@
+[Desktop Entry]
+Version=1.0
+Terminal=false
+Icon=jemboss
+Exec=runJemboss.csh
+Name=Jemboss
+GenericName=GUI for EMBOSS
+Comment=Graphical user interface for the European Molecular Biology Open Software Suite.
+Type=Application
+Categories=Biology;Science;Education;
--- emboss-6.4.0.orig/debian/gbp.conf
+++ emboss-6.4.0/debian/gbp.conf
@@ -0,0 +1,9 @@
+# The source package of emboss is managed with git-buildpackage and pristine-tar.
+
+[DEFAULT]
+# use pristine-tar:
+pristine-tar = True
+
+[git-dch]
+# include 7 digits of the commit ID in the changelog entry:
+id-length = 7
--- emboss-6.4.0.orig/debian/README.debian
+++ emboss-6.4.0/debian/README.debian
@@ -0,0 +1,47 @@
+EMBOSS for Debian
+=================
+
+Some programs renamed
+---------------------
+
+Some programs in EMBOSS have a name which is also used by other programs from
+other packages. The Debian distribution does not allow two packages to conflict
+in this way. Therfore 'cons' has been renamed 'em_cons' and 'pscan has been
+renamed 'em_pscan'.
+
+There is a directory in which the program names are guaranteed to be always
+unchanged, /usr/lib/emboss. You can prepend it to your PATH, with a command
+such as 'PATH = /usr/lib/emboss:$PATH' with Bourne shells, so that when you run
+'cons' or 'pscan', it is always the EMBOSS program.  Other programs could be
+renamed in the future, so it is strongly recommended to use this path in your
+scripts.
+
+
+tfm uses Debian's pager by default
+----------------------------------
+
+The `tfm' program will use /usr/bin/pager instead of /usr/bin/more by default.
+/usr/bin/pager is managed via the `update-alternatives' utility and can point
+to other pagers such as `less' and `most'. This can be overridden by using the
+PAGER environment variable, just as in default EMBOSS installations.
+
+
+EMBOSS Quick Guide relicenced
+-----------------------------
+
+This package contains a relicenced version of the EMBOSS Quick Guide. Its
+uuencoded sources (in MS Word format) are included in the Debian source package
+'emboss'.
+
+
+Notes about how this package is tested
+--------------------------------------
+
+The EMBOSS packages for Debian are tested during the build process by running
+the regression checks of the ‘test/qa/qatest.csh’ script. You can consult the
+results in the build logs available at ‘http://buildd.debian.org/emboss’. In
+addition, the packages are tested locally by the developer performing the
+upload, by running a couple of very simple programs like ‘embossversion’ and
+‘tfm’.
+
+ -- Charles Plessy <plessy@debian.org>  Fri, 07 Mar 2008 10:23:12 +0900
--- emboss-6.4.0.orig/debian/README.source
+++ emboss-6.4.0/debian/README.source
@@ -0,0 +1,8 @@
+This packages uses a patch system. Please read
+/usr/share/doc/quilt/README.source for more informations.
+
+The binary packages are built against the zlib and expat library distributed in
+Debian, not the conveniences copies co-distributed with EMBOSS. This is done by:
+
+ - passing ‘--enable-systemlibs’ to the configure command.
+ - passing ‘LDFLAGS="-lexpat"’ to the make command.
--- emboss-6.4.0.orig/debian/jemboss.menu
+++ emboss-6.4.0/debian/jemboss.menu
@@ -0,0 +1,4 @@
+?package(jemboss):needs="X11" section="Applications/Science/Biology" \
+	title="Jemboss" \
+	description="Graphical user interface for the European Molecular Biology Open Software Suite." \
+	command="runJemboss.csh"
--- emboss-6.4.0.orig/debian/emboss-data.install
+++ emboss-6.4.0/debian/emboss-data.install
@@ -0,0 +1 @@
+debian/emboss_tmp/usr/share/EMBOSS usr/share
--- emboss-6.4.0.orig/debian/emboss.sharedmimeinfo
+++ emboss-6.4.0/debian/emboss.sharedmimeinfo
@@ -0,0 +1,21 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<mime-info xmlns='http://www.freedesktop.org/standards/shared-mime-info'>
+        <mime-type type="application/vnd.appliedbiosystems.abif">
+                <alias type="application/x-dna"/>
+                <alias type="application/abi1"/>
+                <comment>ABIF chromatogram</comment>
+                <!-- alternative: ABIF format -->
+                <!-- decide yourself -->
+                <acronym>ABIF</acronym>
+                <expanded-acronym>Applied Biosystems, Inc. Format</expanded-acronym>
+                <!-- Format spec available at
+http://www.appliedbiosystems.com/support/software_community/ABIF_File_Format.pdf -->
+                <!-- offset 4 and 5 stand for the version number -->
+                <magic priority="50">
+                        <match type="string" offset="0"
+                               value="ABIF??tdir"
+                               mask="0xffffffff0000ffffffff"/>
+                </magic>
+                <glob pattern="*.ab1"/>
+        </mime-type>
+</mime-info>
--- emboss-6.4.0.orig/debian/copyright
+++ emboss-6.4.0/debian/copyright
@@ -0,0 +1,201 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Source: ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-6.4.0.tar.gz
+
+Files: *
+Copyright: The EMBOSS developers or their employers.
+License: emboss
+ EMBOSS License (http://emboss.sourceforge.net/licence/)
+ .
+ The AJAX and NUCLEUS libraries are released under the GNU Library General
+ Public Licence.
+ .
+ The EMBOSS Administrator’s Guide can be copied, distributed and/or modified
+ under the terms of the GNU Free Documentation License, Version 1.1 or any
+ later version published by the Free Software Foundation; with no Invariant
+ Sections, with no Front-Cover Texts, and with no Back-Cover Texts.  A copy of
+ the license is included in the chapter entitled ”GNU Free Documentation
+ License”.
+ .
+ The EMBOSS Quick Guide has been relicenced and can be used, modified and
+ distributed under the same terms as EMBOSS itself.
+ .
+ EMBOSS applications are released under the GNU General Public Licence.
+ .
+ Parsing of ACD files does not constitute a "derived work" and developers are
+ encouraged to do this, for example to write their own GUIs.
+ .
+ For developers who have their own licensing conditions already in effect, there
+ will be an additional way to contribute. The EMBASSY collection can include
+ packages that use the EMBOSS core libraries and interfaces but under their own
+ licensing conditions. They will be bound by the Library GPL of the AJAX and
+ NUCLEUS libraries, but not necessarily by the full GPL.
+ .
+ Some of the suggestions and code examples from David Hanson's book
+ "C Interfaces and Implementations" are included in the AJAX library.
+ This library is available from http://www.cs.princeton.edu/software/cii/
+ or ftp://ftp.cs.princeton.edu/pub/packages/cii/
+ .
+ The COPYRIGHT file in release 1.10 says:
+ .
+ > The author of this software is David R. Hanson.
+ > 
+ > Copyright (c) 1994,1995,1996 by David R. Hanson. All Rights Reserved.
+ > 
+ > Permission to use, copy, modify, and distribute this software for any
+ > purpose, subject to the provisions described below, without fee is
+ > hereby granted, provided that this entire notice is included in all
+ > copies of any software that is or includes a copy or modification of
+ > this software and in all copies of the supporting documentation for
+ > such software.
+ > 
+ > THIS SOFTWARE IS BEING PROVIDED "AS IS", WITHOUT ANY EXPRESS OR IMPLIED
+ > WARRANTY. IN PARTICULAR, THE AUTHOR DOES MAKE ANY REPRESENTATION OR
+ > WARRANTY OF ANY KIND CONCERNING THE MERCHANTABILITY OF THIS SOFTWARE OR
+ > ITS FITNESS FOR ANY PARTICULAR PURPOSE.
+ > 
+ > David Hanson / drh@cs.princeton.edu / http://www.cs.princeton.edu/~drh/
+ > Wed Apr 24 13:44:16 PDT 1996
+ > Mon Dec 12 15:58:13 EST 1994
+Comment: On Debian systems, the complete text of the GNU General Public License
+ version 2, the GNU Free Documentation License version 1.2, and the GNU Library
+ Public License version 2 can be found in ‘/usr/share/common-licenses/GPL-2’,
+ ‘/usr/share/common-licenses/GFDL-1.2’ and ‘/usr/share/common-licenses/LGPL-2’
+ respectively.
+
+Files: ajax/pcre/*
+Copyright: © 1997-2000 University of Cambridge
+License: PCRE
+ PCRE is a library of functions to support regular expressions whose syntax
+ and semantics are as close as possible to those of the Perl 5 language.
+ .
+ Written by: Philip Hazel <ph10@cam.ac.uk>
+ .
+ University of Cambridge Computing Service,
+ Cambridge, England. Phone: +44 1223 334714.
+ .
+ Copyright (c) 1997-2000 University of Cambridge
+ .
+ Permission is granted to anyone to use this software for any purpose on any
+ computer system, and to redistribute it freely, subject to the following
+ restrictions:
+ .
+  1. This software is distributed in the hope that it will be useful,
+     but WITHOUT ANY WARRANTY; without even the implied warranty of
+     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ .
+  2. The origin of this software must not be misrepresented, either by
+     explicit claim or by omission. In practice, this means that if you use
+     PCRE in software which you distribute to others, commercially or
+     otherwise, you must put a sentence like this
+ .
+       Regular expression support is provided by the PCRE library package,
+       which is open source software, written by Philip Hazel, and copyright
+       by the University of Cambridge, England.
+ .
+     somewhere reasonably visible in your documentation and in any relevant
+     files or online help data or similar. A reference to the ftp site for
+     the source, that is, to
+ .
+       ftp://ftp.csx.cam.ac.uk/pub/software/programming/pcre/
+ .
+     should also be given in the documentation.
+ .
+  3. Altered versions must be plainly marked as such, and must not be
+     misrepresented as being the original software.
+ .
+  4. If PCRE is embedded in any software that is released under the GNU
+     General Purpose Licence (GPL), then the terms of that licence shall
+     supersede any condition above with which it is incompatible.
+
+Files: plplot/*
+Copyright: © 1987, 1988 by Digital Equipment Corporation, Maynard, Massachusetts,
+    © 1991, 1993, 1994  Wesley Ebisuzaki
+           © 1992, 1993, 1994, 1995, 2001, 2002, 2004  Maurice LeBrun
+           © 1992, 1999, 2001  Geoffrey Furnish  
+           © 1992,  Maurice J. LeBrun, Geoff Furnish, Tony Richardson.
+           © 2000, 2001, 2002, 2004, 2005  Alan W. Irwin 
+           © 2000, 2001, 2002, 2003, 2004 Joao Cardoso
+           © 2001, 2003, 2004, 2005  Rafael Laboissiere
+           © 2001, 2002, 2003, 2004  Andrew Roach
+           © 2002,  Vincent Darley
+           © 2004, 2005  Thomas J. Duck
+           © 2004, 2005, 2006  Andrew Ross
+           © 2006,  Hazen Babcock
+           © 2006,  Jim Dishaw
+           © 2006, Werner Smekal
+License: GPL-2+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Library General Public
+ License as published by the Free Software Foundation; either
+ version 2 of the License, or (at your option) any later version.
+ .
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+ Library General Public License for more details.
+ .
+ You should have received a copy of the GNU Library General Public
+ License along with this library; if not, write to the Free Software
+ Foundation, Inc. 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+
+Files: ajax/zlib/*
+Copyright: © 1995-2005 Jean-loup Gailly and Mark Adler
+License: zlib
+  This software is provided 'as-is', without any express or implied
+  warranty.  In no event will the authors be held liable for any damages
+  arising from the use of this software.
+ .
+  Permission is granted to anyone to use this software for any purpose,
+  including commercial applications, and to alter it and redistribute it
+  freely, subject to the following restrictions:
+ .
+  1. The origin of this software must not be misrepresented; you must not
+     claim that you wrote the original software. If you use this software
+     in a product, an acknowledgment in the product documentation would be
+     appreciated but is not required.
+  2. Altered source versions must be plainly marked as such, and must not be
+     misrepresented as being the original software.
+  3. This notice may not be removed or altered from any source distribution.
+ .
+  Jean-loup Gailly        Mark Adler
+  jloup@gzip.org          madler@alumni.caltech.edu
+
+Files: doc/programs/html/antigenic.html
+ doc/programs/html/pasteseq.html
+ doc/programs/html/showpep.html
+ doc/programs/master/emboss/apps/inc/acdc.input
+ doc/programs/master/emboss/apps/inc/acdlog.input
+ doc/programs/master/emboss/apps/inc/acdtrace.input
+ doc/programs/master/emboss/apps/inc/antigenic.input
+ doc/programs/master/emboss/apps/inc/pasteseq.input
+ doc/programs/master/emboss/apps/inc/showpep.input
+ doc/programs/text/antigenic.txt
+ doc/programs/text/pasteseq.txt
+ doc/programs/text/showpep.txt
+ emboss/data/dbxref.txt
+ test/data/amir.swiss
+ test/data/uniprotft.sw
+ test/swiss/seq.dat
+ test/swnew/trembl.dat
+Copyright: none
+ These files are marked to be copyrighted by the UniProt Consortium, but this
+ applies to the UniProt database as a whole, not to the individual records.
+License: not-the-CC-BY-ND-3.0
+ Despite the following statement:
+ .
+  Copyrighted by the UniProt Consortium, see http://www.uniprot.org/terms
+  Distributed under the Creative Commons Attribution-NoDerivs License
+ .
+ The above files, as individual records, are not copyrighted.  The statement is
+ for the UniProt as a whole.
+
+Files: debian/*
+Copyright: the developers
+License: unclear
+ The EMBOSS package for Debian was initially prepared by Matt Hope
+ (dopey@debian.org) in 2002-2004 and released on
+ (http://debian.bioinformatics.unsw.edu.au/). The package distributed in Debian
+ was prepared by the "pkg-emboss" project in 2006, using the work of Matt Hope
+ as a starting point. The packaging work of the pkg-emboss project is in the
+ public domain unless stated otherwise.
+
--- emboss-6.4.0.orig/debian/upstream
+++ emboss-6.4.0/debian/upstream
@@ -0,0 +1,17 @@
+Contact: EMBOSS core development team <emboss-bug@emboss.open-bio.org>
+Homepage: http://emboss.sourceforge.net
+Name: EMBOSS
+Reference:
+ title: >
+  EMBOSS: The European Molecular Biology Open Software Suite
+ journal: Trends in Genetics
+ volume: 16
+ number: 6
+ pages: 276 - 277
+ year: 2000
+ issn: 0168-9525
+ url: http://www.sciencedirect.com/science/article/B6TCY-40CRS27-G/2/b4e5945c07c58d5a1257cbd685971317
+ author: Peter Rice and Ian Longden and Alan Bleasby
+ PMID: 10827456
+ DOI: 10.1016/S0168-9525(00)02024-2
+Watch: ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-([\d.]*)\.tar\.gz
--- emboss-6.4.0.orig/debian/emboss.dirs
+++ emboss-6.4.0/debian/emboss.dirs
@@ -0,0 +1,4 @@
+usr/bin
+#usr/share/applications
+etc/emboss/embossrc.d
+usr/share/man/man1
--- emboss-6.4.0.orig/debian/changelog
+++ emboss-6.4.0/debian/changelog
@@ -0,0 +1,501 @@
+emboss (6.4.0-2.5.201403212318) ucs4-0-0-0; urgency=low
+
+  * UCS auto build. No patches were applied to the original source package
+
+ -- Univention builddaemon <buildd@univention.de>  Fri, 21 Mar 2014 23:18:26 +0100
+
+emboss (6.4.0-2) unstable; urgency=low
+
+  * Separate architecture-dependant and independant targets in debian/rules.
+    This makes the package buildable again on our build farm.
+
+ -- Charles Plessy <plessy@debian.org>  Thu, 21 Jun 2012 14:31:59 +0900
+
+emboss (6.4.0-1) unstable; urgency=low
+
+  [ Charles Plessy ]
+  * New upstream release.
+  * Removed calls to dh_makeshlibs in debian/rules (closes: #595613).
+  * Build on libpng-dev instead of libpng12-dev (closes: #662313).
+  * Breaks: EMBASSY <= 6.3.1 (debian/control).
+
+  [ Andreas Tille ]
+  * debian/upstream: separate reference section
+  * debian/rules:
+     - Make sure every binary package has a changelog file
+     - enable hardening
+     - do not clean backup file which is part of upstream tarball
+     - remove executable flag from some test data
+     - restore executable flag of some jemboss utils which seems to
+       be removed by install target
+  * debian/control:
+     - remove article from description
+     - Standards-Version: 3.9.3 (no changes needed)
+  * debian/emboss.menu: delete - chances that users will pick command
+    line programs from longish menu entries are pretty low
+  * debian/emboss-lib.lintian-overrides: Adapted string of lintian
+    warning
+
+ -- Charles Plessy <plessy@debian.org>  Wed, 20 Jun 2012 18:55:16 +0900
+
+emboss (6.3.1-6) unstable; urgency=low
+
+  * All EMBOSS libraries are to be considered private. The libajax* and
+    libnucleus* are merged in the emboss-lib package, which is moved
+    from the ‘libs’ to the ‘science’ section. Closes: #595613.
+  * Added a Lintian override for the convenience copy of the PCRE
+    library (debian/emboss-lib.lintian-overrides).
+  * Build-depend on libhpdf-dev for PDF support, removed erroneous build
+    dependance on libpcre3-dev (debian/control).
+  * Added dependance on emboss to jemboss (debian/control).
+
+ -- Charles Plessy <plessy@debian.org>  Thu, 16 Sep 2010 21:06:14 +0900
+
+emboss (6.3.1-5) unstable; urgency=low
+
+  * New upstream patch, version 1-4.
+  * Restore original config.* files in the clean target if the unpacked
+    source package is a git repository (debian/rules).
+
+ -- Charles Plessy <plessy@debian.org>  Thu, 12 Aug 2010 08:00:58 +0900
+
+emboss (6.3.1-4) unstable; urgency=low
+
+  * New upstream patch, version 1-2.
+  * Unset LS_COLORS in debian/rules (see #592089).
+
+ -- Charles Plessy <plessy@debian.org>  Sat, 07 Aug 2010 23:03:10 +0900
+
+emboss (6.3.1-3) unstable; urgency=low
+
+  * Use default Java instead of OpenJDK (debian/control, debian/rules,
+    closes: #590553, thanks to Petr Salinger).
+  * Incremented Standards-Version in debian/control to reflect conformance
+    with Debian Policy 3.9.1 (no changes needed).
+
+ -- Charles Plessy <plessy@debian.org>  Wed, 28 Jul 2010 23:42:31 +0900
+
+emboss (6.3.1-2) unstable; urgency=low
+
+  * First upstream patch for version 6.3.1 (debian/series,
+    debian/patches/official-upstream-patch.patch).
+  * Moved openjdk-6-jdk to Build-Depends (debian/control, closes: #589897).
+
+ -- Charles Plessy <plessy@debian.org>  Fri, 23 Jul 2010 10:51:50 +0900
+
+emboss (6.3.1-1) unstable; urgency=low
+
+  * New upstream release.
+    - Dropped debian/patches/official-upstream-patch.patch.
+    - Refreshed the manual pages (debian/*manpages*).
+  * Incremented Standards-Version in debian/control to reflect conformance
+    with Debian Policy 3.9.0 (no changes needed).
+  * Keep and restore a clean copy of the test directory, closes: #587170.
+  * Build against Debian's zlib and expat libraries (debian/rules,
+    debian/control, deleted debian/libajax6.lintian-overrides).
+  * Added support for MySQL and PostgreSQL (debian/control, debian/rules).
+  * Added symbols files for emboss-libs, libajax6 and libnucleus6. This
+    will prevent mixing incompatible binary packages (LP: 526356).
+
+ -- Charles Plessy <plessy@debian.org>  Wed, 21 Jul 2010 15:24:07 +0900
+
+emboss (6.2.0-2) unstable; urgency=low
+
+  * Updated debian/patches/official-upstream-patch.patch to version 1-19.
+
+ -- Charles Plessy <plessy@debian.org>  Tue, 22 Jun 2010 17:01:44 +0900
+
+emboss (6.2.0-1) unstable; urgency=low
+
+  * New upstream release.
+  * Dropped useless dependency on csh | c-shell for emboss (LP: 525662).
+  * Incremented Standards-Version in debian/control to reflect conformance
+    with Policy 3.8.4 (no changes needed).
+  * Detected a zlib convenience copy; added debian/emboss.lintian-overrides
+    until Upstream confirms that EMBOSS can build on latest pristine zlib
+    (See http://lists.open-bio.org/pipermail/emboss/2010-May/003915.html).
+
+ -- Charles Plessy <plessy@debian.org>  Mon, 31 May 2010 15:13:09 +0900
+
+emboss (6.1.0-5) unstable; urgency=low
+
+  * The source package is now managed with Git (debian/control).
+    - VCS URLs updated in debian/control.
+  * debian/changelog: corrected an error on a program name (vectorstrip).
+  * debian/patches/transient-vectorstrip.patch: keep quality scores.
+  * Two new patches not yet officialised:
+    - debian/patches/transient-vectorstrip.patch: retain quality scores.
+    - debian/patches/tfm-html.patch: corrects path to HTML documentation.
+  * Added Debian and FreeDesktop menu entries for Jemboss.
+  * Do not create a makefile when there is not at clean time (debian/rules).
+  * Documented how the package is tested in README.debian.
+  * Added various informations about Upstream in debian/upstream-metadata.yaml
+
+ -- Charles Plessy <plessy@debian.org>  Mon, 09 Nov 2009 20:39:28 +0900
+
+emboss (6.1.0-4) unstable; urgency=low
+
+  * New upstream patch (patch-1-2):
+    - Fix string extension so that pointers in lists remain valid.
+    - This fixes a bug in processing SwissProt complex descriptions.
+    - Fix definition of AJRESIZE0 macro.
+    - Fix processing of first match in a profile alignment (prophet).
+  * Delete /usr/share/EMBOSS/doc/programs/text/frestdist.txt, that
+    should belong to embassy-phylip (PHYLIPNEW). (debian/rules)
+  * Incremented Standards-Version in debian/control to reflect conformance
+    with Policy 3.8.3 (no changes needed).
+  * Removed the libtool libraries from the development packages (debian/rules).
+
+ -- Charles Plessy <plessy@debian.org>  Tue, 25 Aug 2009 23:19:10 +0900
+
+emboss (6.1.0-2) unstable; urgency=low
+
+  * New upstream patch (patch-1-1):
+    - Fix feature specification problems in Jemboss.
+    - Use version number to point to documentation URLs
+    - Remove standalone option from server script.
+    - Correct FASTQ input searching for '@' to start next sequence
+    - Standardize FASTQ sequence formats with other OpenBio projects
+    - Correct issues in igstrict, genpept and refseqp formats
+  * debian/control:
+    - Incremented Standards-Version to reflect conformance with Policy 3.8.2
+      (no changes needed). 
+  * debian/copyright.introduction:
+    - Use symbolic links to refer to relevant versions of the GNU licenses.
+
+ -- Charles Plessy <plessy@debian.org>  Sat, 01 Aug 2009 10:26:26 +0900
+
+emboss (6.1.0-1) unstable; urgency=low
+
+  * New upstream release (Closes: #530112).
+  * Dropped patch against previous release.
+  * Created or refreshed the manpages.
+
+ -- Charles Plessy <plessy@debian.org>  Wed, 15 Jul 2009 23:15:26 +0900
+
+emboss (6.0.1-11) unstable; urgency=low
+
+  * New upstream patch (patch-1-12):
+    - Remove the 'aligned' attribute that was added in Fix 4.
+    - Fix crash if maxfragl > 40 selected.
+    - Update Entrez retrieval to cope with an extra line added
+      in the NCBI results.
+    - For phylogenetic applications (PHYLIPNEW) reading distance matrix files
+      failed for some formats written by other applications. Distance matrix
+      input now works for multiple matrices in square, upper-triangular and
+      lower-triangular formats.
+
+ -- Charles Plessy <plessy@debian.org>  Sun, 17 May 2009 14:51:05 +0900
+
+emboss (6.0.1-10) unstable; urgency=low
+
+  * New upstream patch (patch-1-8):
+      Incorrect information was often given in the subsidiary table
+      listing REs that would cut a greater number of times than an
+      optional user-supplied maximum number. The main role of
+      the program was unaffected.
+
+ -- Charles Plessy <plessy@debian.org>  Tue, 21 Apr 2009 13:01:38 +0900
+
+emboss (6.0.1-9) unstable; urgency=low
+
+  * New upstream patch (patch-1-7):
+    - Corrections on syntax using the master qualifier name as a suffix.
+    - Better support of the --without-x (not used in this package).
+    - Bug corrected for needle and water using the -nobrief option.
+  * debian/rules
+    - Corrected again the targets to avoid calling them when it is not
+      necessary.
+    - Defines emboss_acdroot, emboss_docroot and emboss_data in order
+      to run the tests.
+
+ -- Charles Plessy <plessy@debian.org>  Wed, 08 Apr 2009 20:20:58 +0900
+
+emboss (6.0.1-8) unstable; urgency=low
+
+  * debian/rules:
+     - Do not pass java options to the configure script if openjdk is not
+       installed (Closes: #521996, thanks to Peter Green).
+     - Recursive removal of emboss_tmp (to build the package twice in a row).
+     - Removed one `dh binary-indep` instance that strangely sneaked in after
+       running `svn update`.
+  * debian/control:
+    - Moved again openjdk-6-jdk to Build-Depends-Indep.
+    - Added debhelper's ${misc:Depends} substitution variable to the packages
+      that did not already depend on it.
+
+ -- Charles Plessy <plessy@debian.org>  Tue, 31 Mar 2009 14:26:55 +0900
+
+emboss (6.0.1-7) unstable; urgency=low
+
+  * debian/control: moved openjdk-6-jdk to Build-Depends.
+    Apologies to buildd administrators. (Closes: #521912).
+
+ -- Charles Plessy <plessy@debian.org>  Tue, 31 Mar 2009 08:34:59 +0900
+
+emboss (6.0.1-6) unstable; urgency=low
+
+  * debian/rules:
+    - Build arch all packages only when binary-indep is called
+      (Closes: #521398)
+    - Corrected stamping gymnastics.
+  * debian/control: moved openjdk-6-jdk to Build-Depends-Indep 
+
+ -- Charles Plessy <plessy@debian.org>  Mon, 30 Mar 2009 13:02:11 +0900
+
+emboss (6.0.1-5) unstable; urgency=low
+
+  * New upstream patch (patch-1-6): correction for large pairwise alignments.
+  * debian/control:
+    - Incremented Standards-Version to reflect conformance with Policy 3.8.1
+      (no changes needed).
+    - Moved the bibliographic reference from the description of the EMBOSS
+      package to the file debian/reference.
+
+ -- Charles Plessy <plessy@debian.org>  Wed, 25 Mar 2009 11:44:30 +0900
+
+emboss (6.0.1-4) unstable; urgency=low
+
+  * New upstream patch (patch-1-5):
+    - removes unnecessary whitespaces in edialign.acd.
+    - saves Citations and comments in EMBL/GenBank formats for each new
+      entry processed.
+  * debian/control:
+    - Uses the official homepage URL as confirmed by Upstream.
+    - Redundant section field removed for jemboss.
+    - Description corrected for libnucleus6-dev.
+  * debian/rules:
+     - Pass --bindir=/usr/lib/emboss directly instead of moving files.
+     - Hardcode AJAX_FIXED_ROOT to /usr/share/EMBOSS (Closes: #487539).
+     - Replaced `dh_clean -k', deprecated, by dh_prep.
+  * debian/emboss.dir, debian/emboss.install: simplified after reworking
+    the installation of the binaries and their symbolic links.
+
+ -- Charles Plessy <plessy@debian.org>  Sun, 22 Feb 2009 22:53:55 +0900
+
+emboss (6.0.1-3) experimental; urgency=low
+
+  * New upstream patch (patch-1-3).
+    - fixes segmentation fault in vectorstrip when -auto is used with empty
+      vectorsfile.
+    - adds '.' trailer to the OS line in SwissProt output.
+  * debian/rules: corrected the section of the manual pages of the renamed
+    programs from 1 to 1e (Closes: #503733).
+  * Preliminary support for jEMBOSS:
+    - Build-Depend on openjdk-6-jdk (debian/control).
+    - New package "jemboss", depending on openjdk-6-jre (debian/control).
+    - The jemboss package contains everything installed by the command
+      `make -C jemboss install' (debian/rules).
+
+ -- Charles Plessy <plessy@debian.org>  Wed, 26 Nov 2008 08:57:20 +0900
+
+emboss (6.0.1-2) experimental; urgency=low
+
+  * New upstream patch (patch-1-1).
+    - jaspscan can now scan multiple sequences.
+    - "digest -allpartials" now reports all C-term fragments.
+
+ -- Charles Plessy <plessy@debian.org>  Wed, 27 Aug 2008 22:11:45 +0900
+
+emboss (6.0.1-1) experimental; urgency=low
+
+  * New upstream release:
+    - New applications: aligncopy, aligncopypair, consambig, density,
+      featcopy, featreport, infobase, inforesidue, jaspextract, jaspscan,
+      maskambignuc, maskambigprot, nohtml, nospace, notab, sizeseq,
+      skipredundant, trimspace.
+    - See `/usr/share/doc/emboss/changelog.gz' for more details.
+  * debian/patches:
+    - Removed the patches that are obsoleted by the new release.
+    - Documented the local patch on `tfm' that changes default pager.
+  * debian/README.source added to document how to patch and unpatch the
+    sources.
+  * debian/emboss-doc.doc-base.{apps/groups} corrected for new file locations.
+  * debian/control:
+    - Replaced build dependency on deprecated x-dev by x11proto-core-dev.
+    - Uses debhelper 7.
+    - Incremented the soname of the AJAX and NUCLEUS libraries (conflict and
+      replace the previous versions).
+    - Incremented Standards-Version to 3.8.0 after adding README.Sources.
+    - Added a new package, emboss-test, that contains test data.
+    - Build-Depends: tcsh | csh | c-shell to run the tests.
+  * debian/rules:
+    - Implemented build-time tests.
+    - Updated the instructions to build manpages.
+
+ -- Charles Plessy <plessy@debian.org>  Thu, 17 Jul 2008 14:07:40 +0900
+
+emboss (5.0.0-7) unstable; urgency=low
+
+  * Changed the doc-base section according to the new policy.
+  * Updated my email address.
+  * Updated the contact address in the manpages.
+
+ -- Charles Plessy <plessy@debian.org>  Fri, 16 May 2008 19:58:37 +0900
+
+emboss (5.0.0-6) unstable; urgency=low
+
+  * New bugfixes released upstream:
+    - Fixes failure on some databases if the PAGESIZE was set large
+      and the CACHESIZE was set small.
+    - Platform-independence modifications added.
+  * debian/README.Debian: described the change of default pager for tfm.
+
+ -- Charles Plessy <charles-debian-nospam@plessy.org>  Fri, 07 Mar 2008 10:15:31 +0900
+
+emboss (5.0.0-5) unstable; urgency=low
+
+  * New bugfixes released upstream.
+    - Fixes changed ID format in GCG databases.
+    - Fixes reading from PIR databases.
+    - Fixes a problem with O in protein sequences for pyrrolysine.
+    - Fixes a problem in GENBANK output format.
+    - Fixes a problem in reading protein sequences from Staden
+      "spin" interface.
+    - Fixes tokens that are longer than the maximum length.
+    - debian/patches now uses the monolithic upstream patch instead of
+      file-per-file fixes. You can find longer explanations in the header
+      of debian/patches/patch-1-3.
+
+ -- Charles Plessy <charles-debian-nospam@plessy.org>  Sat, 01 Mar 2008 11:46:26 +0900
+
+emboss (5.0.0-4) unstable; urgency=low
+
+  * debian/patches:
+    - using-pager-in-tfm.patch:
+      Patching tfm so that it uses the alternatives system `/usr/bin/pager'
+      if the `PAGER' environment variable is not defined.
+    - embindex-fix-2008-01-19.patch:
+      Official fix 3. EMBOSS-5.0.0/nucleus/embindex.c 18 Jan 2008.
+      Order and fill fixes to sort out potential problems with kw/de/tx
+      indexes.
+
+ -- Charles Plessy <charles-debian-nospam@plessy.org>  Wed, 23 Jan 2008 20:56:22 +0900
+
+emboss (5.0.0-3) unstable; urgency=low
+
+  [ Nelson A. de Oliveira ]
+  * Using bzip2 compression for packages. This saves about 832KB of space.
+
+  [ Charles Plessy ]
+  * debian/patches/ajindex-fix-2008-01-09.patch:
+    - Fixes rare secondary index problem with input files over 2Gb.
+  * debian/control:
+    - Switched maintainership to the Debian-Med packaging team.
+    - Relocated the package to the Debian-Med Subversion repository.
+    - Allowed upload by Debian Maintainers.
+    - Checked that the package is compliant to Policy 3.7.3
+    - Added dialign again to the Recommends: field. It only disappeared from
+      the documentation; the edialign program is still there.
+    - -dev packages now depend on their corresponding libraries.
+    - Replaced occurrences of $(source:Version} by ${binary:Version} to make
+      the packages binNMU safe.
+    - emboss-data and emboss-doc do not Suggest: emboss anymore.
+    - Changed the description of libajax5 and libnucleus5 so that they are not
+      identical.
+    - Removed the XS- prefix in the Vcs fields.
+    - Build-depends on autotools-dev.
+  * debian/rules:
+    - Removes Makefiles ignored by make distclean in the test directory.
+    - Uses config.(sub|guess) from the autotools-dev package.
+
+ -- Charles Plessy <charles-debian-nospam@plessy.org>  Thu, 10 Jan 2008 21:27:31 +0900
+
+emboss (5.0.0-2) unstable; urgency=low
+
+  [ Charles Plessy ]
+  * Using a emboss/psiphi.c file fixed by upstream
+    ftp://emboss.open-bio.org/pub/EMBOSS/fixes/psiphi.c
+  * Documentation:
+    - Building the manpages offline to save buildd time, therefore not
+      depending anymore on the XML toolchain.
+    - Added a "e" suffix to the manpages, to avoid conflicts.
+      (Closes: #427439)
+    - Linked /usr/share/emboss-doc/doc/ to /usr/share/EMBOSS/docs, and
+      registered documentation in doc-base. (Closes: #423941)
+  * Gave their own packages to the AJAX and NUCLEUS libraries.
+    - Header files are in /usr/include/ajax and /usr/include/nucleus.
+    - The private pcre files are kept under /usr/include/ajax. (Closes: #433316)
+  * Packaging:
+    - Removed the extra Tag field in debian/control.
+    - Removed the recommendation on dialign, as edialign disappeared.
+    - Tightened the Depends: relationship between emboss and
+      emboss-lib (Closes: #435232).
+    - Removed inactive developer from the uploaders list.
+    - Suggests: embassy.
+  * Temporarily incorporates a relicenced version of the EMBOSS Quick
+    Guide, until it becomes part of the original tarball. Its sources
+    are shipped uuencoded, therefore emboss now build-depends on sharutils.
+
+  [ Nelson A. de Oliveira ]
+  * Checked and fixed clean target. (Closes: #442554).
+
+ -- Charles Plessy <charles-debian-nospam@plessy.org>  Sat, 13 Oct 2007 15:05:53 +0900
+
+emboss (5.0.0-1) unstable; urgency=low
+
+  * New upstream version
+  * Renaming cons and pscan to em_cons and em_pscan, see README.Debian
+    for more information.
+  * Moved all the binaries to /usr/lib/emboss. /usr/bin contains only
+    symbolic links (Closes : #427439, #427440).
+  * Makes sure that there is a Makefile before invoking the clean rule.
+  * Added /etc/emboss/embossrc.d directory for future modular
+    configuration.
+  * Switched from dpatch to quilt (no patches for the moment).
+  * Build-depend on libemboss-acd-perl to generate manpages with
+    acd2docbook.pl, written especially for this package (Closes: #423938).
+  * Adding a placeholder file to force the inclusion of debian/manpages.
+  * Removing the entries in the Debian menu until we agree that we
+    want them.
+
+ -- Charles Plessy <charles-debian-nospam@plessy.org>  Thu, 19 Jul 2007 13:56:11 +0900
+
+emboss (4.1.0-1) experimental; urgency=low
+
+  * New maintainer and uploaders
+  * First official release (Closes: #156276)
+  * Xlib transition.
+  * Using dpatch and /usr/share/dpatch/dpatch.make to manage patches.
+  * Added XS-Vcs entries in debian/changelog.
+  * Removed the pcre includes from the emboss-libs package.
+  * Fixed watch file.
+  * Emboss Recommends:dialign and Suggests:clustalw. 
+
+ -- Charles Plessy <charles-debian-nospam@plessy.org>  Mon, 12 Mar 2007 08:26:15 +0900
+
+emboss (2.8.0-2) unstable; urgency=low
+
+  * Fixed manpages being in both emboss and emboss-lib
+  * Removed circ.dep. emboss <-> emboss-lib
+
+ -- Matt Hope <dopey@debian.org>  Fri, 21 May 2004 12:47:47 +1000
+
+emboss (2.8.0-1) unstable; urgency=low
+
+  * New upstream release
+
+ -- Matt Hope <dopey@debian.org>  Fri,  5 Dec 2003 15:08:54 +1100
+
+emboss (2.7.1-1) unstable; urgency=low
+
+  * New upstream release
+  * emboss-lib
+    - Fixed the shlibs.
+
+ -- Matt Hope <matth@bioinformatics.unsw.edu.au>  Mon,  7 Jul 2003 14:36:14 +1000
+
+emboss (2.6.0-1) unstable; urgency=low
+
+  * New upstream release
+
+ -- Matt Hope <matth@bioinformatics.unsw.edu.au>  Fri,  7 Apr 2003 21:41:12 +1000
+
+emboss (2.4.1-1) unstable; urgency=low
+
+  * Initial package.
+    Thanks for the feedback from everyone.
+    (Closes: Bug#156276 ITP)
+
+ -- Matt Hope <matth@bioinformatics.unsw.edu.au>  Sat,  6 Jul 2002 01:11:17 +1000
+
--- emboss-6.4.0.orig/debian/emboss-test.dirs
+++ emboss-6.4.0/debian/emboss-test.dirs
@@ -0,0 +1,2 @@
+usr/share/EMBOSS
+etc/emboss/embossrc.d
--- emboss-6.4.0.orig/debian/EMBOSS_qg.doc.uu
+++ emboss-6.4.0/debian/EMBOSS_qg.doc.uu
@@ -0,0 +1,1460 @@
+begin 644 EMBOSS_qg.doc
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--- emboss-6.4.0.orig/debian/EMBOSS_qg_new.pdf.uu
+++ emboss-6.4.0/debian/EMBOSS_qg_new.pdf.uu
@@ -0,0 +1,2718 @@
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+M("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`*("`@("`@("`@
+M("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@
+M("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@
+M(`H@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@
+M("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@
+M("`@("`@("`@("`@"B`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@
+M("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@
+M("`@("`@("`@("`@("`@("`@("`@("`*("`@("`@("`@("`@("`@("`@("`@
+M("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@
+M("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@(`H@("`@("`@("`@
+M("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@
+M("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@
+M"B`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@
+M("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@
+M("`@("`@("`@("`*("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@
+M("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@
+M("`@("`@("`@("`@("`@("`@("`@(`H@("`@("`@("`@("`@("`@("`@("`@
+M("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@
+M("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@"B`@("`@("`@("`@
+M("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@
+M("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`*
+M("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@
+M("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@
+M("`@("`@("`@(`H@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@
+M("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@
+M("`@("`@("`@("`@("`@("`@("`@"B`@("`@("`@("`@("`@("`@("`@("`@
+M("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@
+M("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`*("`@("`@("`@("`@
+M("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@
+M("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@(`H@
+M("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@
+M("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@
+M("`@("`@("`@"B`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@
+M("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@
+M("`@("`@("`@("`@("`@("`@("`*("`@("`@("`@("`@("`@("`@("`@("`@
+M("`@"CP_>'!A8VME="!E;F0](G<B/SX-96YD<W1R96%M#65N9&]B:@TQ.2`P
+M(&]B:CP\+T-R96%T:6]N1&%T92A$.C(P,#<Q,#`Y,38Q-3`V*S`Q)S`P)RDO
+M075T:&]R*$1A=FED($UA<G1I;BDO0W)E871O<BA7;W)D.B!C9W!D9G1O<',@
+M0U504R!F:6QT97(I+U!R;V1U8V5R*$%C<F]B870@1&ES=&EL;&5R(#<N,"XU
+M(&9O<B!-86-I;G1O<V@I+TUO9$1A=&4H1#HR,#`W,3`P.3$V,34P-BLP,2<P
+M,"<I+U1I=&QE*$UI8W)O<V]F="!7;W)D("T@14U"3U-37W%G+F1O8RD^/@UE
+M;F1O8FH->')E9@TP(#(P#3`P,#`P,#`P,#`@-C4U,S4@9@T*,#`P,#`V,S`U
+M.2`P,#`P,"!N#0HP,#`P,#8S,3DS(#`P,#`P(&X-"C`P,#`P-C,S,S@@,#`P
+M,#`@;@T*,#`P,#`W-C`W-R`P,#`P,"!N#0HP,#`P,#DQ-S4P(#`P,#`P(&X-
+M"C`P,#`P.3$Y-3@@,#`P,#`@;@T*,#`P,#$P.30R-2`P,#`P,"!N#0HP,#`P
+M,3`Y-C(X(#`P,#`P(&X-"C`P,#`Q,34X.#4@,#`P,#`@;@T*,#`P,#$Q-C`Y
+M,2`P,#`P,"!N#0HP,#`P,3$V,C0Y(#`P,#`P(&X-"C`P,#`Q,38U.3,@,#`P
+M,#`@;@T*,#`P,#$Q-S$P-B`P,#`P,"!N#0HP,#`P,3$W,C8T(#`P,#`P(&X-
+M"C`P,#`Q,3<W,#4@,#`P,#`@;@T*,#`P,#$Q-S<T,"`P,#`P,"!N#0HP,#`P
+M,3$W-S8T(#`P,#`P(&X-"C`P,#`Q,3<X,C(@,#`P,#`@;@T*,#`P,#$R,30U
+M,2`P,#`P,"!N#0IT<F%I;&5R#3P\+U-I>F4@,C`^/@US=&%R='AR968-,3$V
+'#24E14]&#0``
+`
+end
--- emboss-6.4.0.orig/debian/emboss-doc.doc-base.emboss-qg
+++ emboss-6.4.0/debian/emboss-doc.doc-base.emboss-qg
@@ -0,0 +1,11 @@
+Document: emboss-qg
+Title: EMBOSS, a quick guide.
+Author: David Martin, EMBnet Norway
+Abstract: Summary of emboss programs and their options on a recto-verso page.
+Section: Science/Biology
+
+Format: PostScript
+Files: /usr/share/doc/emboss-doc/doc/manuals/emboss_qg.ps
+
+Format: PDF
+Files: /usr/share/doc/emboss-doc/doc/manuals/emboss_qg.pdf
--- emboss-6.4.0.orig/debian/jemboss.install
+++ emboss-6.4.0/debian/jemboss.install
@@ -0,0 +1 @@
+debian/jemboss.desktop	usr/share/applications
--- emboss-6.4.0.orig/debian/reference
+++ emboss-6.4.0/debian/reference
@@ -0,0 +1,16 @@
+@article{Rice2000276,
+title = "EMBOSS: The European Molecular Biology Open Software Suite",
+journal = "Trends in Genetics",
+volume = "16",
+number = "6",
+pages = "276 - 277",
+year = "2000",
+note = "",
+issn = "0168-9525",
+doi = "DOI: 10.1016/S0168-9525(00)02024-2",
+url = "http://www.sciencedirect.com/science/article/B6TCY-40CRS27-G/2/b4e5945c07c58d5a1257cbd685971317",
+author = "Peter Rice and Ian Longden and Alan Bleasby",
+keywords = "Bioinformatics",
+keywords = "Database",
+keywords = "EMBOSS"
+}
--- emboss-6.4.0.orig/debian/emboss-doc.doc-base.domainatrix
+++ emboss-6.4.0/debian/emboss-doc.doc-base.domainatrix
@@ -0,0 +1,13 @@
+Document: domainatrix
+Title: Domainatrix guide.
+Abstract: This document describes the  use  of  EMBOSS  applications  in  the  EMBASSY
+ package domainatrix.  Most of these directly or indirectly make use  of  the
+ protein structure databases pdb and scop.   All  of  the  applications  here
+ were written by Jon Ison, Ranjeeva Ranasinghe, Matt Blades  and  Waqas  Awan
+ and coordinated by  Jon  Ison  to  whom  enquiries  should  be  sent  (email
+ jison@hgmp.mrc.ac.uk).  This software is part of  an  experimental  analysis
+ pipeline and we provide it  in  the  hope  that  it  will  be  useful.
+Section: Science/Biology
+
+Format: Text
+Files: /usr/share/doc/emboss-doc/doc/manuals/domainatrix.txt
--- emboss-6.4.0.orig/debian/control
+++ emboss-6.4.0/debian/control
@@ -0,0 +1,96 @@
+Source: emboss
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Charles Plessy <plessy@debian.org>,
+ Nelson A. de Oliveira <naoliv@debian.org>,
+ Andreas Tille <tille@debian.org>
+Build-Depends: debhelper (>= 9), quilt, libx11-dev, x11proto-core-dev,
+ libgdchart-gd2-xpm-dev, zlib1g-dev, libpng-dev, libexpat1-dev, libhpdf-dev,
+ libmysqlclient-dev, libpq-dev, antiword, sharutils, autotools-dev,
+ tcsh | csh | c-shell,
+# Needed until the following is solved: https://sourceforge.net/tracker/?func=detail&aid=3033326&group_id=93650&atid=605031 
+ default-jdk
+#Build-Depends-Indep: default-jdk
+Vcs-Browser: http://git.debian.org/?p=debian-med/emboss.git
+Vcs-Git: git://git.debian.org/git/debian-med/emboss.git
+Standards-Version: 3.9.3
+Homepage: http://emboss.sourceforge.net
+
+Package: emboss
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}, emboss-lib (= ${binary:Version}), emboss-data (= ${source:Version})
+Recommends: primer3, dialign
+Suggests: emboss-doc, emboss-test, embassy, clustalw
+Description: european molecular biology open software suite
+ EMBOSS is a free Open Source software analysis package specially developed for
+ the needs of the molecular biology (e.g. EMBnet) user community. The software
+ automatically copes with data in a variety of formats and even allows
+ transparent retrieval of sequence data from the web. Also, as extensive
+ libraries are provided with the package, it is a platform to allow other
+ scientists to develop and release software in true open source spirit. EMBOSS
+ also integrates a range of currently available packages and tools for sequence
+ analysis into a seamless whole. EMBOSS breaks the historical trend towards
+ commercial software packages.
+
+Package: emboss-data
+Architecture: all
+Depends: ${misc:Depends}
+Description: data files for the EMBOSS package
+ This package includes data files needed by EMBOSS, the European Molecular
+ Biology Open Software Suite.
+
+Package: emboss-doc
+Section: doc
+Architecture: all
+Depends: ${misc:Depends}
+Suggests: pdf-viewer | postscript-viewer
+Description: documentation for EMBOSS
+ This package includes non-essential user documentation for EMBOSS, the
+ European Molecular Biology Open Software Suite.
+
+Package: emboss-test
+Section: misc
+Architecture: all
+Depends: ${misc:Depends}
+Recommends: tcsh | csh | c-shell
+Suggests: valgrind
+Description: test files for the EMBOSS package
+ This package includes test files for EMBOSS, the European Molecular Biology
+ Open Software Suite.
+ .
+ It is a good idea to use the data from this package for your bug reports when
+ possible.
+
+Package: emboss-lib
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Conflicts: libajax5, libajax6, libajax5-dev, libajax6-dev, libnucleus5, libnucleus6, libnucleus5-dev, libnucleus6-dev
+Replaces: libajax5, libajax6, libajax5-dev, libajax6-dev, libnucleus5, libnucleus6, libnucleus5-dev, libnucleus6-dev
+Breaks: embassy-domainatrix (<= 0.1.0+20100721-3), embassy-domalign (<= 0.1.0+20100721-3),
+ embassy-domsearch (<= 0.1.0++20100721-3), embassy-phylip (<= 3.69+20100721-3)
+Description: EMBOSS Libraries
+ This package contains the core libraries of the European Molecular Biology
+ Open Software Suite, EMBOSS.
+ .
+ AJAX covers standard data structures, including strings, sequences, file
+ handles, queues, hashes, heaps, lists, dictionaries, trees and dynamic
+ arrays. It also covers standard algorithms including comparisons, pattern
+ matching, sorting, and iterators. AJAX will also provide a set of high level
+ graphics functions suited to the needs of sequence analysis applications.
+ .
+ The NUCLEUS library provides higher-level functions specific to molecular
+ sequence analysis, including sequence comparisons, translation, codon usage
+ and annotation.
+ .
+ It also contains a eplplot, an EMBOSS, a fork of the plplot library.
+ .
+ In Debian, these libraries are to be considered private.
+
+Package: jemboss
+Architecture: all
+Depends: ${shlibs:Depends}, ${misc:Depends}, emboss, default-jre, tcsh | csh | c-shell
+Description: graphical user interface to EMBOSS
+ Jemboss is a Graphical User Interface (GUI) to EMBOSS, the European Molecular
+ Biology Open Software Suite. It is part of the EMBOSS distribution.
--- emboss-6.4.0.orig/debian/emboss-doc.dirs
+++ emboss-6.4.0/debian/emboss-doc.dirs
@@ -0,0 +1 @@
+usr/share/EMBOSS/doc
--- emboss-6.4.0.orig/debian/jemboss.dirs
+++ emboss-6.4.0/debian/jemboss.dirs
@@ -0,0 +1 @@
+/usr/bin
--- emboss-6.4.0.orig/debian/emboss-java.dirs
+++ emboss-6.4.0/debian/emboss-java.dirs
@@ -0,0 +1 @@
+usr/bin usr/share/EMBOSS/jemboss/org/
--- emboss-6.4.0.orig/debian/emboss-doc.doc-base.emboss-admin
+++ emboss-6.4.0/debian/emboss-doc.doc-base.emboss-admin
@@ -0,0 +1,24 @@
+Document: emboss-admin
+Title: The EMBOSS Administrator’s Guide
+Author: David Martin, EMBnet Norway
+ Peter Rice, LION Bioscience
+ Alan Bleasby, HGMP (EMBnet UK)
+Section: Science/Biology
+Abstract: This guide has been written to assist system administrators and developers
+ with the installation and configuration of EMBOSS. If you are reading this to
+ find out how to do bioinformatics then you are wasting your time. You are
+ referred instead to the Resources chapter below where there is a list of more
+ relevant literature and web sites. Experienced users may find this document
+ useful for configuring their own databases and customising their EMBOSS
+ experience.
+ .
+ This guide relates to EMBOSS 2.5.0
+
+Format: PostScript
+Files: /usr/share/doc/emboss-doc/doc/manuals/admin.ps
+
+Format: PDF
+Files: /usr/share/doc/emboss-doc/doc/manuals/admin.pdf
+
+Format: DVI
+Files: /usr/share/doc/emboss-doc/doc/manuals/admin.dvi
--- emboss-6.4.0.orig/debian/emboss-data.dirs
+++ emboss-6.4.0/debian/emboss-data.dirs
@@ -0,0 +1 @@
+usr/share/EMBOSS
--- emboss-6.4.0.orig/debian/emboss-doc.doc-base.emboss-apps
+++ emboss-6.4.0/debian/emboss-doc.doc-base.emboss-apps
@@ -0,0 +1,9 @@
+Document: emboss-apps
+Title: EMBOSS Applications
+Author: The EMBOSS Developpers
+Section: Science/Biology
+Abstract: Documentation of the EMBOSS applications sorted in alphabetical order. 
+
+Format: HTML
+Index: /usr/share/doc/emboss-doc/doc/programs/html/index.html
+Files: /usr/share/doc/emboss-doc/doc/programs/html/*.html
--- emboss-6.4.0.orig/debian/emboss-lib.lintian-overrides
+++ emboss-6.4.0/debian/emboss-lib.lintian-overrides
@@ -0,0 +1,8 @@
+# EMBOSS unfortunately uses a modified copy of the PCRE library. Upstream
+# understands the problems it causes for us, but will not remove it in the
+# short term. The other embedded and modified library is PLplot. Thanks
+# to Upstream's efforts, the emboss packages in Debian can be built
+# against Debian's zlib and expat libraries instead of the convenience code
+# copies in the original upstream sources.
+# -- Charles Plessy <plessy@debian.org>  Thu, 16 Sep 2010 20:27:09 +0900
+emboss-lib: embedded-library usr/lib/emboss/lib/libepcre.so.7.0.9: pcre3
\ No newline at end of file
--- emboss-6.4.0.orig/debian/emboss-doc.links
+++ emboss-6.4.0/debian/emboss-doc.links
@@ -0,0 +1 @@
+usr/share/EMBOSS/doc	usr/share/doc/emboss-doc/doc
--- emboss-6.4.0.orig/debian/rules
+++ emboss-6.4.0/debian/rules
@@ -0,0 +1,114 @@
+#!/usr/bin/make -f
+
+export DH_VERBOSE=1
+
+%:
+	dh $@ --with autotools-dev,quilt
+
+VERSION := $(shell dpkg-parsechangelog | grep Ver | cut -d' ' -f2 | cut -d- -f1)
+RENAMED := cons pscan
+
+EMBOSS-TMP  = $(CURDIR)/debian/emboss_tmp
+EMBOSS      = $(CURDIR)/debian/emboss
+EMBOSS-TEST = $(CURDIR)/debian/emboss-test
+EMBOSS-LIB  = $(CURDIR)/debian/emboss-lib
+
+CONFFLAGS    = --bindir=/usr/lib/emboss
+CONFFLAGS   += --libdir=/usr/lib/emboss/lib
+CONFFLAGS   += --includedir=/usr/lib/emboss/include
+CONFFLAGS   += --enable-systemlibs
+CONFFLAGS   += --with-java=/usr/lib/jvm/default-java/include
+CONFFLAGS   += --with-javaos=/usr/lib/jvm/default-java/include/linux
+
+CPPFLAGS:=$(shell dpkg-buildflags --get CPPFLAGS)
+CFLAGS:=$(shell dpkg-buildflags --get CFLAGS)
+
+DEB_LDFLAGS += -lexpat
+DEB_LDFLAGS += $(shell mysql_config --libs)
+DEB_LDFLAGS += -lpq
+DEB_LDFLAGS += $(shell dpkg-buildflags --get LDFLAGS)
+#DEB_LDFLAGS += $(shell pg_config  | grep LIBS | cut -f2 -d=)
+
+override_dh_auto_configure:
+	dh_autotools-dev_updateconfig
+	dh_auto_configure -- $(CONFFLAGS)
+	
+override_dh_auto_build:
+	dh_auto_build -- AJAX_FIXED_ROOT=\\\"/usr/share/EMBOSS\\\" CPPFLAGS="$(CPPFLAGS)" CFLAGS="$(CFLAGS)" LDFLAGS="$(DEB_LDFLAGS)"
+
+override_dh_clean:
+	dh_autotools-dev_restoreconfig
+	rm --force --recursive debian/emboss_tmp
+	find jemboss/ -type f -name "*.class" | xargs -r rm -f
+	[ ! -d debian/testbackup ] || ( $(RM) --recursive test ; mv debian/testbackup test )
+	dh_clean  --exclude=feattext.html~ config.status test-stamp install-stamp
+
+override_dh_auto_install-arch:
+	### Binaries and data go to a temporary dir before being moved to their own package ###
+	$(MAKE) -C emboss install DESTDIR=$(EMBOSS-TMP)
+
+	# Make symbolic links from /usr/bin to /usr/lib/emboss
+	cd $(EMBOSS)/usr/bin/ ; \
+		for i in $(EMBOSS-TMP)/usr/lib/emboss/* ; \
+		do ln -sf ../lib/emboss/`basename $$i` . ; \
+		done
+
+	### Renaming conflicting binaries (see also in binary-arch) ###
+	for i in $(RENAMED) ; \
+		do mv $(EMBOSS)/usr/bin/$$i $(EMBOSS)/usr/bin/em_$$i ; \
+		done
+
+	### EMBOSS libraries go in the emboss-lib package. ###
+	$(MAKE) -C ajax install DESTDIR=$(EMBOSS-LIB)
+	$(MAKE) -C nucleus install DESTDIR=$(EMBOSS-LIB)
+	$(MAKE) -C plplot install DESTDIR=$(EMBOSS-LIB)
+	find $(EMBOSS-LIB)/usr/lib -name '*.la' -exec rm {} \;
+
+	### Documentation goes in emboss-doc. ###
+	$(MAKE) -C doc install DESTDIR=$(CURDIR)/debian/emboss-doc
+	antiword $(CURDIR)/debian/emboss-doc/usr/share/EMBOSS/doc/manuals/domainatrix.doc > $(CURDIR)/debian/emboss-doc/usr/share/EMBOSS/doc/manuals/domainatrix.txt
+	# Remove this file when the relicenced file becomes part of the upstream tarball.
+	uudecode -o $(CURDIR)/debian/emboss-doc/usr/share/EMBOSS/doc/manuals/EMBOSS_qg.pdf $(CURDIR)/debian/EMBOSS_qg_new.pdf.uu
+
+override_dh_auto_install-indep:
+	$(MAKE) -C jemboss install DESTDIR=$(CURDIR)/debian/jemboss bindir=/usr/bin
+	# install target seems to remove executable flag which is claimed by lintian
+	find $(CURDIR)/debian/jemboss/usr/share/EMBOSS/jemboss/utils -type f -not -executable -name "*sh" -exec chmod a+x \{\} \;
+	# dangling LICEN[CS]E FILE
+	rm $(CURDIR)/debian/jemboss/usr/share/EMBOSS/jemboss/LICENSE
+
+	### Installation of the test suite
+	cp -a test $(CURDIR)/debian/emboss-test/usr/share/EMBOSS/
+	sed -i "/SET emboss_tempdata/cSET emboss_tempdata /usr/share/EMBOSS/test" $(CURDIR)/debian/emboss-test/usr/share/EMBOSS/test/.embossrc
+	sed -i "/SET emboss_qadata/cSET emboss_qadata /usr/share/EMBOSS/test" $(CURDIR)/debian/emboss-test/usr/share/EMBOSS/test/.embossrc
+	mv $(CURDIR)/debian/emboss-test/usr/share/EMBOSS/test/.embossrc $(CURDIR)/debian/emboss-test/etc/emboss/embossrc.d/emboss-test
+	find $(CURDIR)/debian/emboss-test/usr/share/EMBOSS/test/data -executable -type f -exec chmod a-x \{\} \;
+
+override_dh_auto_test:
+	$(RM) test-stamp
+	[ -d debian/testbackup ] || cp -a test debian/testbackup
+	sed -i "/SET emboss_tempdata/cSET emboss_tempdata $(CURDIR)/test" test/.embossrc
+	sed -i "/SET emboss_qadata/cSET emboss_qadata $(CURDIR)/test" test/.embossrc
+	echo "SET emboss_acdroot $(CURDIR)/emboss/acd" >> test/.embossrc
+	echo "SET emboss_data $(CURDIR)/emboss/data" >> test/.embossrc
+	echo "SET emboss_docroot $(CURDIR)/doc" >> test/.embossrc
+	cd test/qa && LS_COLORS='' EMBOSSRC=$(CURDIR)/test PATH=$(CURDIR)/emboss:$$PATH EMBOSS_ROOT=../../../ ./qatest.csh
+	
+override_dh_installchangelogs:
+	dh_installchangelogs -k ChangeLog
+	
+override_dh_installman:
+	dh_installman -a -p emboss
+	for i in $(RENAMED) ; \
+		do dh_link usr/share/man/man1/$$i.1e.gz usr/share/man/man1/em_$$i.1e.gz ; \
+		done
+	
+override_dh_builddeb:
+	dh_builddeb -- -Z xz
+
+
+# Target to refresh the manpages; needs libemboss-acd-perl, xsltproc, docbook-xml and docbook-xsl
+manpages: debian/manpages/success
+debian/manpages/success:
+	debian/build-manpages.sh
+	echo "The manpages have been sucessfully built" > debian/manpages/success
--- emboss-6.4.0.orig/debian/acd2docbook.pl
+++ emboss-6.4.0/debian/acd2docbook.pl
@@ -0,0 +1,167 @@
+#!/usr/bin/perl -w
+
+# acd2docbook.pl was made for Debian by Charles Plessy in 2007, and can be
+# used, modified and redistributed as if it were in the public domain.
+#
+# You can report bugs to bugs.debian.org/emboss, and access the latest version here:
+# http://svn.debian.org/wsvn/pkg-emboss/emboss/trunk/debian/acd2docbook.pl?op=file&rev=0&sc=0
+#
+# Many thanks to David Bauer for the original idea.
+
+use strict;
+use warnings;
+
+use EMBOSS::ACD;
+
+my $acdfile = shift; 
+my $embossversion = shift;
+my $date = qx(date -R);
+chop $date;
+
+my $acd = EMBOSS::ACD->new($acdfile) ;
+
+my $name = $acd->name or die "No name !";
+my $NAME = $name;
+$NAME =~ s/(.)/\U$1/g;
+my $purpose = $acd->documentation;
+my $groups = join(",", $acd->groups);
+
+print <<"__XML__";
+<?xml version='1.0' encoding='ISO-8859-1'?>
+<?xml-stylesheet type="text/xsl"
+	href="http://docbook.sourceforge.net/release/xsl/current/manpages/docbook.xsl"?>
+<!DOCTYPE refentry PUBLIC "-//OASIS//DTD DocBook XML V4.5//EN"
+	"http://www.oasis-open.org/docbook/xml/4.5/docbookx.dtd" [
+
+<!-- Autogenerated by the acd2docbook.pl script from the emboss Debian package.    -->
+<!-- Template from docbook-xsl version 1.72.0.dfsg.1-1                             -->
+
+  <!ENTITY dhemail     "debian-med-packaging\@lists.alioth.debian.org">
+  <!ENTITY dhusername  "Debian Med Packaging Team">
+  <!ENTITY dhrelease   "$embossversion">
+  <!ENTITY dhtitle     "EMBOSS Manual for Debian">
+  <!ENTITY dhucpackage "$NAME">
+  <!ENTITY dhpackage   "$name">
+  <!ENTITY dhproduct   "EMBOSS">
+  <!ENTITY dhsection   "1e">
+]>
+
+<refentry>
+	<refentryinfo>
+		<title>&dhtitle;</title>
+		<productname>&dhproduct;</productname>
+		<releaseinfo role="version">&dhrelease;</releaseinfo>
+		<authorgroup>
+			<author>
+				<othername>&dhusername;</othername>
+				<contrib>Wrote the script used to autogenerate this manual page.</contrib>
+				<address>
+					<email>&dhemail;</email>
+				</address>
+			</author>
+		</authorgroup>
+		<legalnotice>
+			<para>This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package. It can be redistributed under the same terms as EMBOSS itself.</para>
+		</legalnotice>
+	</refentryinfo>
+
+	<refmeta>
+		<refentrytitle>&dhucpackage;</refentrytitle>
+		<manvolnum>&dhsection;</manvolnum>
+	</refmeta>
+
+	<refnamediv>
+		<refname>&dhpackage;</refname>
+		<refpurpose>$purpose</refpurpose>
+	</refnamediv>
+
+	<refsynopsisdiv>
+		<cmdsynopsis>
+			<command>&dhpackage;</command>
+__XML__
+
+foreach my $parameter ( $acd->param) {
+	next if $$parameter{datatype} =~ /section/;
+	my ($paraname, $argname, $paratype) = ( $$parameter{name}, $$parameter{datatype}, $$parameter{type} );
+	my $additional = 'choice="plain"';
+	$additional = 'choice="opt"' if $$parameter{additional} eq 'Y';
+	print qq(\t\t\t<arg $additional><option>-$paraname <replaceable>$argname</replaceable></option></arg>\n);
+}
+
+
+print <<"__XML__";
+		</cmdsynopsis>
+		<cmdsynopsis>
+			<command>&dhpackage;</command>
+			<arg choice="plain"><option>-help</option></arg>
+		</cmdsynopsis>
+	</refsynopsisdiv>
+	<refsect1 id="description">
+		<title>DESCRIPTION</title>
+		<para><command>&dhpackage;</command> is a command line program from EMBOSS (<quote>the European Molecular Biology Open Software Suite</quote>). It is part of the "$groups" command group(s). 
+		</para>
+	</refsect1>
+
+	<refsect1 id="options">
+			<!-- Use the variablelist.term.separator and the
+			     variablelist.term.break.after parameters to
+			     control the term elements. -->
+		<title>OPTIONS</title>
+__XML__
+
+foreach my $parameter( $acd->param) {
+
+	# Does a section begin ?
+	if ($$parameter{datatype} eq "section") {
+		print qq(\t\t<refsect2 id="$$parameter{name}">\n\t\t\t<title>$$parameter{information}</title>\n\t\t\t<variablelist>\n);
+		next;
+	}
+
+	# Does a section end ?
+	if ($$parameter{datatype} eq "endsection") {
+		print "\t\t\t</variablelist>\n\t\t</refsect2>\n";
+		next;
+	}
+
+	# Is there a Default value ?
+	my $default = '';
+	$default = " Default value: $$parameter{default}" if $$parameter{default};
+
+	# Use entities when necessary:
+	$$parameter{help} =~ s/&/&amp;/g ;
+	$$parameter{help} =~ s/</&lt;/g ;
+	$$parameter{help} =~ s/>/&gt;/g ;
+        $default =~ s/&/&amp;/g ;
+        $default =~ s/</&lt;/g ;
+        $default =~ s/>/&gt;/g ;
+
+
+
+	print<<"__XML__";
+				<varlistentry>
+					<term>
+						<option>-$$parameter{name}</option>
+						<parameter>$$parameter{datatype}</parameter>
+					</term>
+					<listitem>
+						<para>$$parameter{help}$default</para>
+					</listitem>
+				</varlistentry>
+__XML__
+}
+
+print<<"__XML__";
+	</refsect1>
+
+	<refsect1 id="bugs">
+		<!-- Or use this section to tell about upstream BTS. -->
+		<title>BUGS</title>
+		<para>Bugs can be reported to the Debian Bug Tracking system (http://bugs.debian.org/emboss), or directly to the EMBOSS developers (http://sourceforge.net/tracker/?group_id=93650&amp;atid=605031).</para>
+	</refsect1>
+
+	<refsect1 id="see_also">
+		<title>SEE ALSO</title>
+		<para>&dhpackage; is fully documented via the <citerefentry><refentrytitle>tfm</refentrytitle><manvolnum>1</manvolnum></citerefentry> system.</para>
+	</refsect1>
+</refentry>
+__XML__
--- emboss-6.4.0.orig/debian/patches/series
+++ emboss-6.4.0/debian/patches/series
@@ -0,0 +1,3 @@
+official-upstream-patch.patch
+using-pager-in-tfm.patch
+tfm-html.patch
--- emboss-6.4.0.orig/debian/patches/using-pager-in-tfm.patch
+++ emboss-6.4.0/debian/patches/using-pager-in-tfm.patch
@@ -0,0 +1,19 @@
+Author: Charles Plessy
+Forwarded: no
+ This patch uses a specificity of Debian.
+Description: Browse the documentation with default pager.
+ `/usr/bin/pager', always exists in Debian and is managed through the
+ alternatives system. With this patch, `tfm' will use `/usr/bin/pager' by
+ default, which points on the user's favorite pager.
+License: as if it were public domain.
+--- emboss-6.4.0.orig/emboss/tfm.c
++++ emboss-6.4.0/emboss/tfm.c
+@@ -87,7 +87,7 @@
+ 	    if(shellpager)
+ 		ajStrAssignC(&pager,shellpager);
+ 	    if(!ajStrGetLen(pager))
+-		ajStrAssignC(&pager,"more");
++		ajStrAssignC(&pager,"pager");
+ 	}
+ 	ajFmtPrintS(&cmd,"%S %S",pager,path);
+ 	ajSysExecPathS(cmd);
--- emboss-6.4.0.orig/debian/patches/tfm-html.patch
+++ emboss-6.4.0/debian/patches/tfm-html.patch
@@ -0,0 +1,14 @@
+Author: Charles Plessy
+Forwarded: https://sourceforge.net/tracker/?func=detail&aid=2877960&group_id=93650&atid=605031
+Description: Corrects the name of the directory where tfm looks for HTML documentation.
+--- emboss-6.4.0.orig/emboss/tfm.c
++++ emboss-6.4.0/emboss/tfm.c
+@@ -231,7 +231,7 @@
+ 	**  if that didn't work then try the doc directory from the
+ 	**  distribution tarball
+ 	*/
+-	ajStrAssignS(docroot, ajNamValueBasedir());
++	ajStrAssignS(docroot, ajNamValueRootdir());
+ 	ajDirnameFix(docroot);
+ 
+ 	if(ajStrGetLen(embassy))
--- emboss-6.4.0.orig/debian/patches/official-upstream-patch.patch
+++ emboss-6.4.0/debian/patches/official-upstream-patch.patch
@@ -0,0 +1,5926 @@
+Description: Official upstream patch.
+  Fix 1. EMBOSS-6.4.0/emboss/dbiflat.c
+         EMBOSS-6.4.0/emboss/dbxflat.c
+ .
+  10-Aug-2011: The SwissProt description line format includes addtional
+  		    tags which interfere with the EMBL parser used in
+  	     previous releases. The fix replaces this with a SwissProt
+  	     parser that strips out the extra tags. After patching the
+  	     release, any existing SwissProt description index files
+  	     should be reindexed. Other indexes are unchanged.
+ .
+  Fix 2. EMBOSS-6.4.0/ajax/core/ajquery.c
+ .
+  10-Aug-2011: For databases with more than one valid format (examples
+  		    include the EBI dbfetch server) this fix allows the
+  		    format to be specified with a qualifier on the command
+  		    line. In the original release only a format in the query
+  		    string was used.
+ .
+ .
+  Fix 3. EMBOSS-6.4.0/ajax/core/ajfeatread.c
+ .
+  10-Aug-2011: When parsing GFF3 format input, long feature tags (for
+  		    example extremely long translations) exceeded limits in
+  		    regular expression parsing. Ths fix decouples testing for
+  		    escaped quotes from the main task of finding quoted
+  		    strings.
+ .
+ .
+  Fix 4. EMBOSS-6.4.0/emboss/data/Etcode.dat
+ .
+  10-Aug-2001: The local data file used by application tcode had a missing
+  		    parameter line.
+ .
+ .
+  Fix 5. EMBOSS-6.4.0/ajax/core/ajrange.c
+ .
+  10-Aug-2011: When sequence ranges (and possible highlighting for
+  		    showalign) were in a list file the parser overwrote
+  		    string values.
+ .
+ .
+  Fix 5. EMBOSS-6.4.0/ajax/core/ajseqabi.c
+ .
+  10-Aug-2011: Sample names in ABI format files were stored in
+  		    incompletely defined strings. This fix corrects the
+  		    string object. The sample name is also used as the
+  		    sequence name.
+ .
+ .
+  Fix 6. EMBOSS-6.4.0/emboss/dbxresource.c
+ .
+  10-Aug-2011: A future change to the format of Data Resource Catalogue
+  		    entries in DRCAT.dat requires an update to the parsing of
+  		    category lines. The current version is not affected.
+ .
+ .
+  Fix 7. EMBOSS-6.4.0/emboss/server.ensemblgenomes
+         EMBOSS-6.4.0/emboss/cacheensembl.c
+         EMBOSS-6.4.0/ajax/ensembl/ensregistry.c
+         EMBOSS-6.4.0/ajax/ensembl/ensregistry.c
+         EMBOSS-6.4.0/ajax/ensembl/ensdatabaseadaptor.c
+         EMBOSS-6.4.0/ajax/ensembl/ensdatabaseadaptor.h
+ .
+  10-Aug-2011: Microbial genomes use an enumerated species code which
+  		    must be added to the query for data retrieval. This fix
+  		    adds the species code to the comment field. In the next
+  		    release a more complete solution will be implemented.
+ .
+ .
+  Fix 8. EMBOSS-6.4.0/ajax/core/ajarch.h
+ .
+  10-Aug-2011: Corrects the size of long integers on Windows systems only.
+ .
+ .
+  Fix 9. EMBOSS-6.4.0/emboss/cirdna.c
+ .
+  10-Aug-2011: Cirdna prints text inside solid blocks invisibly. When
+  	     printed outside the text scaling was too small. The text
+  	     scale is now adjusted for the radius and sequence length
+  	     so that labels should be readable outside the box.
+ .
+ .
+  Fix 10. EMBOSS-6.4.0/ajax/core/ajpat.c
+ .
+  10-Aug-2011: Fuzznuc, fuzzpro and fuzztran using a pattern file
+  	     ignored the command line -mismatch qualifier for the
+  	     first pattern. The default mismatch is now set to this
+  	     value at the start of the pattern matching loop in the
+  	     library.
+ .
+ .
+  Fix 11. EMBOSS-6.4.0/ajax/core/ajfmt.c
+ .
+  11-Aug-2011: ajFmtScanF handled va_list incorrectly. Only noticeable by code
+  	     developers.
+ .
+ .
+  Fix 12. EMBOSS-6.4.0/nucleus/embgroup.c
+ .
+  18-Aug-2011: An internal string variable should be initialised as NULL.
+ .
+ .
+  Fix 13. EMBOSS-6.4.0/ajax/core/ajseqread.c
+ .
+  18-Aug-2011: Reading protein GFF3 files ignored the EMBOSS type comment.
+  	     This appears to be the only way to detect a protein GFF3 file.
+ .
+  Fix 14. EMBOSS-6.4.0/emboss/data/Efeatures.gff3protein
+ .
+  18-Aug-2011: In writing GFF3 protein file, uses the current term name
+  	     from the Sequence Ontology to clear errors from the GFF3
+  	     online validator.
+ .
+  Fix 15. EMBOSS-6.4.0/ajax/core/ajfeatwrite.c
+ .
+  18-Aug-2011: When writing GFF3 format, tags names are explicitly
+  	     converted to lower case as required by the GFF3
+  	     standard. This includes EC_number and /PCR_conditions in
+  	     EMBL/GenBank/DDBJ and several RefseqP tags. The score is
+  	     written using g format to represent very low values.
+ .
+  Fix 16. EMBOSS-6.4.0/ajax/core/ajnexus.c
+  	EMBOSS-6.4.0/ajax/core/ajseqread.c
+ .
+  22-Aug-2011: When reading nexus data format with no taxlabels block
+  	     the attempt to read the taxa (sequence names) from the
+  	     matrix block failed.
+ .
+  Fix 17. EMBOSS-6.4.0/ajax/ajaxdb/ajtextdb.c
+ .
+  22-Aug-2011: The SRS access method added a stray '+' character to the
+  	     getz command line.
+ .
+  Fix 18. EMBOSS-6.4.0/ajax/core/ajquery.c
+ .
+  25-Aug-2011: In some cases a query using a simple identifier
+  	     could try to test an undefined "sv" field.
+ .
+ .
+  Fix 19. EMBOSS-6.4.0/ajax/core/ajseqread.c
+ .
+  02-Sep-2011: Reading "raw" sequence format failed when piped from
+  	     standard input. In release 6.4.0 "raw" format was
+  	     redefined as a binary format to catch binary files that
+  	     start with one or more sequence characters followed by a
+  	     NULL character. This fix continues to check binary files,
+  	     but has to drop the check for data piped through standard
+  	     input which is read as text and cannot be reread as
+  	     binary.
+ .
+  Fix 20. EMBOSS-6.4.0/ajax/core/ajnam.c
+ .
+  02-Sep-2011: Complex database definitions with more than one type or
+  	     format are allowed in 6.4.0 but caused an error message
+  	     from showdb when the type and format were tested.
+ .
+  Fix 21. EMBOSS-6.4.0/emboss/drfinddata.c
+  	EMBOSS-6.4.0/emboss/drfindformat.c
+  	EMBOSS-6.4.0/emboss/drfindid.c
+  	EMBOSS-6.4.0/emboss/drfindresource.c
+ .
+  02-Sep-2011: Running with -debug fails. Debug calls used obsolete datatype
+  	     for data resource internals. Without -debug there was no problem.
+Origin: ftp://emboss.open-bio.org/pub/EMBOSS/fixes/patches/patch-1-21.gz
+Forwarded: not-needed
+--- emboss-6.4.0.orig/ajax/ajaxdb/ajtextdb.c
++++ emboss-6.4.0/ajax/ajaxdb/ajtextdb.c
+@@ -2580,9 +2580,7 @@
+     {
+         field = ajListIterGet(iter);
+ 
+-        if(!nfields)
+-            ajStrAppendK(&textin->Filename, '+');
+-        else
++        if(nfields)
+         {
+             switch(field->Link)
+             {
+@@ -2684,9 +2682,7 @@
+     {
+         field = ajListIterGet(iter);
+ 
+-        if(!nfields)
+-            ajStrAppendK(&textin->Filename, '+');
+-        else
++        if(nfields)
+         {
+             switch(field->Link)
+             {
+--- emboss-6.4.0.orig/ajax/core/ajarch.h
++++ emboss-6.4.0/ajax/core/ajarch.h
+@@ -137,7 +137,7 @@
+ 
+ #ifdef WIN32
+ typedef int ajint;
+-typedef long ajlong;       /* May need to make this long long. */
++typedef long long ajlong;
+ typedef unsigned int ajuint;
+ typedef short ajshort;
+ typedef unsigned short ajushort;
+@@ -159,4 +159,3 @@
+ AJ_END_DECLS
+ 
+ #endif
+-
+--- emboss-6.4.0.orig/ajax/core/ajfeatread.c
++++ emboss-6.4.0/ajax/core/ajfeatread.c
+@@ -3035,7 +3035,8 @@
+     AjPStr  TvString  = NULL;
+     AjPStr  tmptag      = NULL;
+     AjBool  grpset      = ajFalse;
+-    
++    AjBool escapedquote = ajFalse;
++
+     /*ajDebug("featGff3oldProcessTagval '%S'\n",
+       groupfield); */
+     
+@@ -3050,12 +3051,19 @@
+      */
+     
+     ajStrAssignS(&TvString, groupfield);
++    if(ajStrFindC(TvString, "\\\"") >= 0)
++    {
++        escapedquote = ajTrue;
++        ajStrExchangeCC(&TvString, "\\\"", "\001");
++    }
++
+     while(ajStrGetLen(TvString))
+     {
+ 	if(ajRegExec(Gff3oldRegexTvTagval, TvString))
+ 	{
+ 	    ajRegSubI(Gff3oldRegexTvTagval, 1, &tmptag);
+ 	    ajRegSubI(Gff3oldRegexTvTagval, 2, &featinValTmp);
++                
+ 	    ajStrTrimWhite(&featinValTmp);
+ 	    /*ajDebug("Gff3Tv '%S' '%S'\n", tmptag, featinValTmp);*/
+ 	    ajRegPost(Gff3oldRegexTvTagval, &TvString);
+@@ -3076,6 +3084,8 @@
+ 		featFlagSet(gf, featinValTmp);
+ 	    else
+ 	    {
++                if(escapedquote)
++                    ajStrExchangeCC(&featinValTmp, "\001", "\"");
+ 		/*ajDebug("GFF3 before QuoteStrip: '%S'\n", featinValTmp);*/
+ 		ajStrQuoteStrip(&featinValTmp);
+ 		/*ajDebug(" GFF3 after QuoteStrip: '%S'\n", featinValTmp);*/
+@@ -5896,8 +5906,8 @@
+     Gff3Regexdirective = ajRegCompC("^##(.*)");
+     Gff3Regexcomment   = ajRegCompC("^#(.*)");
+     Gff3RegexTvTagval  = ajRegCompC(" *([^ =]+)[ =]([^;]+)*(;|$)"); /* "tag name */
+-    Gff3oldRegexTvTagval  = ajRegCompC(" *([^ =]+)[ =]((\"(\\.|[^\\\"])*\"|"
+-			 	   "[^;]+)*)(;|$)"); /* "tag name */
++    Gff3oldRegexTvTagval  = ajRegCompC(" *([^ =]+)[ =](\"[^\"]*\"|"
++			 	   "[^;]+)(;|$)"); /* "tag name */
+ 
+     FeatInitGff3 = ajTrue;
+ 
+--- emboss-6.4.0.orig/ajax/core/ajfeatwrite.c
++++ emboss-6.4.0/ajax/core/ajfeatwrite.c
+@@ -4134,7 +4134,7 @@
+         tmpid = owner->Seqid;
+ 
+     if(thys->Score)
+-	ajFmtPrintF(file, "%S\t%S\t%S\t%d\t%d\t%.3f\t%c\t%c\t",
++	ajFmtPrintF(file, "%S\t%S\t%S\t%d\t%d\t%.3g\t%c\t%c\t",
+ 	            tmpid,
+ 	            thys->Source,
+ 	            outtyp,
+@@ -4215,6 +4215,7 @@
+     while(!ajListIterDone(iter))
+     {
+ 	tv     = ajListIterGet(iter);
++        ajStrFmtLower(&tv->Tag);
+ 	outtag = tv->Tag;
+ 	
+ 	if(!outtag)
+--- emboss-6.4.0.orig/ajax/core/ajfmt.c
++++ emboss-6.4.0/ajax/core/ajfmt.c
+@@ -50,6 +50,16 @@
+ #include "ajax.h"
+ 
+ 
++#define EVF_PERCENT  1
++#define EVF_NOCON    2
++#define EVF_LONG     4
++#define EVF_AJLONG   8
++#define EVF_UNSIGNED 16
++#define EVF_NEGATE   32
++
++#define EVF_BUF 128
++
++
+ typedef void (*Fmt_T) (ajint code, VALIST ap,
+ 		       int put(int c, void *cl), void *cl,
+ 		       const ajuint* flags, ajint width, ajint precision);
+@@ -148,6 +158,8 @@
+ static void cvt_u(ajint code, VALIST ap, int put(int c, void* cl), void* cl,
+ 		  const ajuint* flags, ajint width, ajint precision);
+ 
++static ajint evfscanf(FILE *stream, const char *fmt, va_list ap);
++
+ 
+ 
+ 
+@@ -2290,7 +2302,7 @@
+     __va_copy(save_ap,ap);
+ #endif
+ 
+-    n = fscanf(file,fmt,ap);
++    n = evfscanf(file,fmt,ap);
+ 
+ #if defined(__amd64__) || defined(__EM64T__) || \
+     defined(__PPC__) && defined(_CALL_SYSV)
+@@ -2304,6 +2316,519 @@
+ }
+ 
+ 
++
++
++/* @funcstatic evfscanf *******************************************************
++**
++** EMBOSS version of C99 vfscanf() including %S conversion
++**
++** @param [r] stream [FILE*] file pointer.
++** @param [r] fmt [const char*] Format string.
++** @param [v] ap [va_list] Variable length argument list
++** @return [ajint] number of successful conversions
++**
++** @release 6.4.0
++** @@
++******************************************************************************/
++
++static ajint evfscanf(FILE *stream, const char *fmt, va_list ap)
++{
++    char fch = '\0';
++    int  ipc = 0;
++    int  tpc = 0;
++    
++    ajuint uflags = 0;
++    ajint  nconv  = 0;
++    ajint  width  = 0;
++    AjBool fin    = ajFalse;
++    AjBool idone  = ajFalse;
++
++    ajulong sum = 0L;
++    
++    ajuint nread = 0;
++    ajint  ret   = EOF;
++    ajint  base  = 10;
++
++    char *p       = NULL;
++    char fchars[] = "0123456789Ee.";
++
++    char buf[EVF_BUF];
++
++    AjPStr *str = NULL;
++    
++    union
++    {
++        ajlong  L;
++        long    l;
++        unsigned long ul;
++        ajulong uL;
++        ajint   i;
++        ajuint  u;
++        char    *c;
++        double  d;
++    } val;
++    
++
++    if(feof(stream))
++        return EOF;
++
++    val.ul = 0L;
++    
++    while((fch = *fmt))
++    {
++        ++fmt;
++
++
++        if(uflags & EVF_PERCENT)
++        {
++            /* If %% has been given then do a simple match */
++            if(fch == '%')
++            {
++                uflags &= ~EVF_PERCENT;
++
++                if((ipc = getc(stream)) == EOF)
++                    break;
++
++                ++sum;
++                
++                if(ipc != (int) fch)
++                    break;
++
++                continue;
++            }
++
++            /* Now in the realm of format specifiers */
++            /* First test for any width */
++
++            if(fch >= '0' && fch <= '0')
++            {
++                fch -= '0';
++
++                if(width == INT_MAX)
++                    width = 0;
++                else
++                    width *= 10;
++
++                width += (ajint) fch;
++
++                continue;
++            }
++            
++            if((char) fch != 'S')
++                fch = tolower(fch);
++
++            switch(fch)
++            {
++                case '*':
++                    uflags |= EVF_NOCON;
++                    continue;
++
++                case 'n':
++                    if(!(uflags & EVF_NOCON))
++                        *(va_arg(ap, ajint *)) = (ajint) sum;
++
++                    break;
++                    
++                case 'c':
++                    if(!(uflags & EVF_NOCON))
++                        val.c = va_arg(ap, char *);
++
++                    if(width == INT_MAX)
++                        width = 1;
++
++                    while(width-- > 0)
++                    {
++                        if((ipc = getc(stream)) == EOF)
++                        {
++                            fin = ajTrue;
++                            break;
++                        }
++
++                        ++nread;
++                        
++                        if(!(uflags & EVF_NOCON))
++                            *val.c++ = (char) ipc;
++                    }
++
++                    break;
++
++                case 'h':      /* ANSI C converts shorts to ints */
++                    continue;
++                    
++                case 'l':
++                    uflags |= EVF_LONG;
++                    continue;
++
++                case 'L':
++                    uflags |= EVF_AJLONG;
++                    continue;
++
++                case 's':
++                    if(!(uflags & EVF_NOCON))
++                        val.c = va_arg(ap, char *);
++
++                    do
++                    {
++                        ipc = getc(stream);
++                        ++sum;
++                    } while(isspace(ipc));
++
++                    if(ipc == EOF)
++                    {
++                        fin = ajTrue;
++                        break;
++                    }
++
++                    while(width-- > 0)
++                    {
++                        if(isspace(ipc))
++                        {
++                            ungetc(ipc, stream);
++                            --sum;
++                            break;
++                        }
++
++                        if(!(uflags & EVF_NOCON))
++                            *val.c++ = (char) ipc;
++
++                        if((ipc = getc(stream)) == EOF)
++                            break;
++
++                        ++nread;
++                    }
++
++                    if(!(uflags & EVF_NOCON))
++                        *val.c = '\0';
++
++                    break;
++
++                case 'S':
++                    if(!(uflags & EVF_NOCON))
++                    {
++                        str = (AjPStr *) va_arg(ap, AjPStr *);
++                        ajStrAssignC(str,"");
++                    }
++                    
++                    do
++                    {
++                        ipc = getc(stream);
++                        ++sum;
++                    } while(isspace(ipc));
++
++                    if(ipc == EOF)
++                    {
++                        fin = ajTrue;
++                        break;
++                    }
++
++                    while(width-- > 0)
++                    {
++                        if(isspace(ipc))
++                        {
++                            ungetc(ipc, stream);
++                            --sum;
++                            break;
++                        }
++
++                        if(!(uflags & EVF_NOCON))
++                            ajStrAppendK(str, (char) ipc);
++
++                        if((ipc = getc(stream)) == EOF)
++                            break;
++
++                        ++nread;
++                    }
++
++                    break;
++
++                case 'o':
++                    base = 8;
++                    /* Fallthrough */
++                case 'x':
++                    if(base == 10)  /* To protect fallthrough from octal */
++                        base = 16;
++                    /* Fallthrough */
++                case 'u':
++                    uflags |= EVF_UNSIGNED;
++                    /* Fallthrough */
++                case 'd':
++                case 'i':
++                    do
++                    {
++                        ipc = getc(stream);
++                        ++sum;
++                    } while(isspace(ipc));
++
++                    if(ipc == EOF)
++                    {
++                        fin = ajTrue;
++                        break;
++                    }
++                    
++                    if((char) ipc == '+' || (char) ipc == '-')
++                    {
++                        if(--width <= 0)
++                        {
++                            fin = ajTrue;
++                            break;
++                        }
++
++                        if((char) ipc == '-')
++                            uflags |= EVF_NEGATE;
++
++                        if((ipc = getc(stream)) == EOF)
++                        {
++                            fin = ajTrue;
++                            break;
++                        }
++
++                        ++sum;
++                    }
++
++                    idone = ajFalse;
++                    val.uL = 0;                    
++
++                    if((char) ipc == '0')
++                    {
++                        if(--width <= 0)
++                            idone = ajTrue;
++
++                        if(!idone)
++                            if((ipc = getc(stream)) == EOF)
++                                idone = ajTrue;
++
++                        if((char) tolower(ipc) == 'x' && !idone)
++                        {
++                            if(fch == 'o' || fch == 'd' || fch == 'u')
++                            {
++                                /* Invalid 0x */
++                                ungetc(ipc, stream);
++                                idone = ajTrue;
++                            }
++
++                            if(!idone)
++                                base = 16;
++
++                            if(!idone)
++                            {
++                                if((ipc = getc(stream)) == EOF)
++                                    idone = ajTrue;
++                                else
++                                    ++sum;
++                            }
++                        }
++                        else if(fch == 'i' && !idone)
++                            base = 8;
++                    }
++
++                    ++nread;
++
++                    for(;!idone;)
++                    {
++                        tpc = tolower(ipc);
++
++                        tpc -= '0';
++
++                        if(tpc > 9)
++                        {
++                            tpc += '0';
++                            tpc -= 'a';
++
++                            if(tpc >= 0)
++                                tpc += 10;
++                        }
++
++                        if(tpc < 0 || tpc >= base)
++                        {
++                            ungetc(ipc, stream);
++                            --nread;
++                            break;
++                        }
++
++                        val.uL *= base;
++                        val.uL += tpc;
++
++                        if(--width <= 0)
++                            break;
++                        
++                        if((ipc = getc(stream)) == EOF)
++                            break;
++
++                        ++nread;
++                    }
++
++                    if((uflags & EVF_NEGATE) && !idone)
++                        val.L = -val.L;
++                    
++                    if(!(uflags & EVF_NOCON))
++                    {
++                        if((uflags & (EVF_UNSIGNED | EVF_AJLONG)) ==
++                            (EVF_UNSIGNED | EVF_AJLONG))
++                            *(va_arg(ap, ajulong *)) = val.uL;
++                        else if(uflags & (EVF_AJLONG))
++                            *(va_arg(ap, ajlong *)) = val.L;
++                        else if((uflags & (EVF_UNSIGNED | EVF_LONG)) ==
++                                 (EVF_UNSIGNED | EVF_LONG))
++                            *(va_arg(ap, unsigned long *)) = val.ul;
++                        else if(uflags & (EVF_LONG))
++                            *(va_arg(ap, long *)) = val.l;
++                        else if(uflags & (EVF_UNSIGNED))
++                            *(va_arg(ap, ajuint *)) = val.u;
++                        else
++                            *(va_arg(ap, ajint *)) = val.i;
++                    }
++
++                    break;
++
++                case 'e':
++                case 'f':
++                case 'g':
++                    do
++                    {
++                        ipc = getc(stream);
++                        ++sum;
++                    } while(isspace(ipc));
++
++                    if(ipc == EOF)
++                    {
++                        --sum;
++                        fin = ajTrue;
++                        break;
++                    }
++                    
++                    if((char) ipc == '+' || (char) ipc == '-')
++                    {
++                        if((char) ipc == '-')
++                            uflags |= EVF_NEGATE;
++
++                        if((ipc = getc(stream)) == EOF)
++                        {
++                            fin = ajTrue;
++                            break;
++                        }
++
++                        ++sum;
++                    }
++
++                    val.d = 0.0;
++
++                    ++nread;
++                    
++                    for(p = buf; p < buf + EVF_BUF - 1 && width >0; --width)
++                    {
++                        if(!strchr(fchars, ipc))
++                        {
++                            ungetc(ipc, stream);
++                            --nread;
++                            break;
++                        }
++
++                        if((char) ipc == 'e' || (char) ipc == 'E')
++                        {
++                            fchars[10] = '\0';
++                            *p++ = (char) ipc;
++
++                            if((ipc = getc(stream)) == EOF)
++                                break;
++
++                            ++nread;
++
++                            if((char) ipc != '+' && (char) ipc != '-')
++                                continue;
++                        }
++                        else if((char) ipc == '.')
++                            fchars[12] = '\0';
++
++                        *p++ = (char) ipc;
++
++                        if((ipc = getc(stream)) == EOF)
++                            break;
++
++                        ++nread;
++                    }
++                    
++                    *p++ = '\0';
++
++                    val.d = strtod(buf, 0);
++                    
++                    if(uflags & EVF_NEGATE)
++                        val.d = -val.d;
++
++                    fchars[10] = 'E';
++                    fchars[12] = '.';
++
++                    *(va_arg(ap, double *)) = val.d;
++
++                    break;
++            }
++
++            if(fin)
++                break;
++            
++            if(nread)
++            {
++                if(!(uflags & EVF_NOCON))
++                    ++nconv;
++
++                ret = 0;
++                sum += nread;
++            }
++            else if(fch != 'n' || ipc == EOF)
++                break;
++
++            uflags = 0;
++        }
++        else if(fch == '%')
++        {
++            uflags = EVF_PERCENT;
++            base = 10;
++            nread = 0;
++            width = INT_MAX;
++        }
++        else if(isspace(fch))
++        {
++            do
++            {
++                ipc = getc(stream);
++                ++sum;
++            } while(isspace(ipc));
++
++            --sum;
++            
++            if(ipc == EOF)
++                break;
++
++            ungetc(ipc, stream);
++        }
++        else
++        {
++            if((ipc = getc(stream)) == EOF)
++                break;
++
++            ++sum;
++            
++            if(ipc != (int) fch)
++                break;
++        }
++
++    }
++
++    if((uflags & EVF_PERCENT) && nread)
++    {
++        if(!(uflags & EVF_NOCON))
++            ++nconv;
++
++        ret = 0;
++    }
++
++    if(ipc == EOF && nconv == 0)
++        return ret;
++    
++    
++    return nconv;
++}
++
++
+ 
+ 
+ /* @funcstatic fmtVscan *******************************************************
+--- emboss-6.4.0.orig/ajax/core/ajnam.c
++++ emboss-6.4.0/ajax/core/ajnam.c
+@@ -8172,6 +8172,10 @@
+     AjBool hasmethod = ajFalse;
+     AjBool hastype   = ajFalse;
+     AjPStr name = NULL;
++    AjPStr token = NULL;
++    AjPStr typetoken = NULL;
++    AjPStrTok handle = NULL;
++    AjPStrTok typehandle = NULL;
+     const AjPStr value = NULL;
+     const AjPStr dbtype = NULL;
+ 
+@@ -8202,9 +8206,22 @@
+ 	    {
+ 		hasformat=ajTrue;
+ 
+-                if(!namInformatTest(value, dbtype))  /* test: dbunknowns.rc */
+-                        namError("Database '%S' %S: '%S' unknown",
+-                                 entry->name, name, value);
++                ok = ajFalse;
++                ajStrTokenAssignC(&typehandle, dbtype, " ,;");
++                ajStrTokenAssignC(&handle, value, " ,;");
++
++                while(ajStrTokenNextParse(&typehandle, &typetoken))
++                {
++                    while(ajStrTokenNextParse(&handle, &token))
++                    {
++                        if(namInformatTest(token, typetoken))
++                            ok = ajTrue;
++                    }
++                }
++
++                if(!ok) /* test: dbunknowns.rc */
++                    namError("Database '%S' %S: '%S' unknown",
++                             entry->name, name, value);
+             }
+ 
+             if(ajStrPrefixC(name, "method"))
+@@ -8221,9 +8238,13 @@
+ 		hastype=ajTrue;
+ 		oktype = ajFalse;
+ 
+-		for(k=0; namDbTypes[k].Name; k++)
+-		    if(ajStrMatchCaseC(value, namDbTypes[k].Name)) 
+-			oktype = ajTrue;
++                ajStrTokenAssignC(&typehandle, value, " ,;");
++                while(ajStrTokenNextParse(&typehandle, &typetoken))
++                {
++                    for(k=0; namDbTypes[k].Name; k++)
++                        if(ajStrMatchCaseC(typetoken, namDbTypes[k].Name)) 
++                            oktype = ajTrue;
++                }
+ 
+ 		if(!oktype)		/* test: dbunknowns.rc */
+ 		    namError("Database '%S' %S: '%S' unknown",
+@@ -8260,6 +8281,10 @@
+     }
+ 
+     ajStrDel(&name);
++    ajStrTokenDel(&handle);
++    ajStrTokenDel(&typehandle);
++    ajStrDel(&token);
++    ajStrDel(&typetoken);
+ 
+     return ok;
+ }
+--- emboss-6.4.0.orig/ajax/core/ajnexus.c
++++ emboss-6.4.0/ajax/core/ajnexus.c
+@@ -2,23 +2,25 @@
+ ** @source AJAX nexus file parsing functions
+ **
+ ** @author Copyright (C) 2003 Peter Rice
+-** @version 1.0
++** @version $Revision: 1.20 $
++** @modified $Date: 2011/08/09 12:03:22 $ by $Author: rice $
+ ** @@
+ **
+ ** This library is free software; you can redistribute it and/or
+-** modify it under the terms of the GNU Library General Public
++** modify it under the terms of the GNU Lesser General Public
+ ** License as published by the Free Software Foundation; either
+-** version 2 of the License, or (at your option) any later version.
++** version 2.1 of the License, or (at your option) any later version.
+ **
+ ** This library is distributed in the hope that it will be useful,
+ ** but WITHOUT ANY WARRANTY; without even the implied warranty of
+ ** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+-** Library General Public License for more details.
++** Lesser General Public License for more details.
++**
++** You should have received a copy of the GNU Lesser General Public
++** License along with this library; if not, write to the Free Software
++** Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
++** MA  02110-1301,  USA.
+ **
+-** You should have received a copy of the GNU Library General Public
+-** License along with this library; if not, write to the
+-** Free Software Foundation, Inc., 59 Temple Place - Suite 330,
+-** Boston, MA  02111-1307, USA.
+ ******************************************************************************/
+ 
+ #include "ajax.h"
+@@ -152,6 +154,8 @@
+ **
+ ** @param [u] buff [AjPFilebuff] Input buffered file
+ ** @return [AjPNexus] Nexus data object
++**
++** @release 2.8.0
+ ** @@
+ ******************************************************************************/
+ 
+@@ -197,6 +201,7 @@
+     if(!ajStrPrefixCaseC(rdline, "#NEXUS"))
+     {				/* first line test */
+ 	ajFilebuffReset(buff);
++        ajStrDel(&rdline);
+ 
+ 	return NULL;
+     }
+@@ -205,7 +210,10 @@
+ 
+     ok = ajBuffreadLine(buff, &rdline);
+     if(!ok)
++    {
++        ajStrDel(&rdline);
+ 	return NULL;
++    }
+ 
+     block = ajFalse;
+     commentlevel = 0;
+@@ -254,7 +262,11 @@
+ 	else if (block && ajRegExec(endexp, rdline)) /* end line */
+ 	{
+ 	    if (!nexusBlockSave(ret, blocklist, blockname))
++            {
++                ajStrDel(&rdline);
++                ajStrDel(&blockname);
+ 		return NULL;
++            }
+ 
+ 	    ajStrAssignClear(&blockname);
+ 	    block = ajFalse;
+@@ -266,9 +278,8 @@
+ 	    if (ajStrGetLen(rdline))
+ 	    {
+ 		ajListstrPushAppend(blocklist, rdline);
++                rdline = NULL;
+ 	    }
+-
+-	    rdline = NULL;
+ 	}
+ 
+ 	ok = ajBuffreadLine(buff, &rdline);
+@@ -277,11 +288,16 @@
+     if (block)
+     {
+ 	ajDebug("ajNexusParse unclosed block '%S'\n", blockname);
+-
++        ajStrDel(&rdline);
++        ajStrDel(&blockname);
+ 	return NULL;
+     }
+ 
+     ajNexusTrace(ret);
++    ajStrDel(&rdline);
++    ajStrDel(&blockname);
++
++    ajListFree(&blocklist);
+ 
+     return ret;
+ }
+@@ -295,6 +311,8 @@
+ **
+ ** @return [AjPNexus] New AjPNexus object
+ ** @category new [AjPNexus] Default constructor
++**
++** @release 2.8.0
+ ******************************************************************************/
+ 
+ AjPNexus ajNexusNew(void)
+@@ -309,12 +327,14 @@
+ 
+ 
+ 
+-/* @funcstatic nexusTaxaNew ***********************************************
++/* @funcstatic nexusTaxaNew ***************************************************
+ **
+ ** Constructor for AjPNexusTaxa
+ **
+ ** @return [AjPNexusTaxa] New AjPNexusTaxa object
+ ** @category new [AjPNexusTaxa] Default constructor
++**
++** @release 2.8.0
+ ******************************************************************************/
+ 
+ static AjPNexusTaxa nexusTaxaNew(void)
+@@ -335,6 +355,8 @@
+ **
+ ** @return [AjPNexusCharacters] New AjPNexusCharacters object
+ ** @category new [AjPNexusCharacters] Default constructor
++**
++** @release 2.8.0
+ ******************************************************************************/
+ 
+ static AjPNexusCharacters nexusCharactersNew(void)
+@@ -363,6 +385,8 @@
+ **
+ ** @return [AjPNexusUnaligned] New AjPNexusUnaligned object
+ ** @category new [AjPNexusUnaligned] Default constructor
++**
++** @release 2.8.0
+ ******************************************************************************/
+ 
+ static AjPNexusUnaligned nexusUnalignedNew(void)
+@@ -389,6 +413,8 @@
+ **
+ ** @return [AjPNexusDistances] New AjPNexusDistances object
+ ** @category new [AjPNexusDistances] Default constructor
++**
++** @release 2.8.0
+ ******************************************************************************/
+ 
+ static AjPNexusDistances nexusDistancesNew(void)
+@@ -409,12 +435,14 @@
+ 
+ 
+ 
+-/* @funcstatic nexusSetsNew ***********************************************
++/* @funcstatic nexusSetsNew ***************************************************
+ **
+ ** Constructor for AjPNexusSets
+ **
+ ** @return [AjPNexusSets] New AjPNexusSets object
+ ** @category new [AjPNexusSets] Default constructor
++**
++** @release 2.8.0
+ ******************************************************************************/
+ 
+ static AjPNexusSets nexusSetsNew(void)
+@@ -435,6 +463,8 @@
+ **
+ ** @return [AjPNexusAssumptions] New AjPNexusAssumptions object
+ ** @category new [AjPNexusAssumptions] Default constructor
++**
++** @release 2.8.0
+ ******************************************************************************/
+ 
+ static AjPNexusAssumptions nexusAssumptionsNew(void)
+@@ -452,12 +482,14 @@
+ 
+ 
+ 
+-/* @funcstatic nexusCodonsNew ***********************************************
++/* @funcstatic nexusCodonsNew *************************************************
+ **
+ ** Constructor for AjPNexusCodons
+ **
+ ** @return [AjPNexusCodons] New AjPNexusCodons object
+ ** @category new [AjPNexusCodons] Default constructor
++**
++** @release 2.8.0
+ ******************************************************************************/
+ 
+ static AjPNexusCodons nexusCodonsNew(void)
+@@ -472,12 +504,14 @@
+ 
+ 
+ 
+-/* @funcstatic nexusTreesNew ***********************************************
++/* @funcstatic nexusTreesNew **************************************************
+ **
+ ** Constructor for AjPNexusTrees
+ **
+ ** @return [AjPNexusTrees] New AjPNexusTrees object
+ ** @category new [AjPNexusTrees] Default constructor
++**
++** @release 2.8.0
+ ******************************************************************************/
+ 
+ static AjPNexusTrees nexusTreesNew(void)
+@@ -492,12 +526,14 @@
+ 
+ 
+ 
+-/* @funcstatic nexusNotesNew ***********************************************
++/* @funcstatic nexusNotesNew **************************************************
+ **
+ ** Constructor for AjPNexusNotes
+ **
+ ** @return [AjPNexusNotes] New AjPNexusNotes object
+ ** @category new [AjPNexusNotes] Default constructor
++**
++** @release 2.8.0
+ ******************************************************************************/
+ 
+ static AjPNexusNotes nexusNotesNew(void)
+@@ -519,6 +555,8 @@
+ ** @param [d] pthys [AjPNexus*] AjPNexus object
+ ** @return [void]
+ ** @category delete [AjPNexus] Default destructor
++**
++** @release 2.8.0
+ ******************************************************************************/
+ 
+ void ajNexusDel(AjPNexus* pthys)
+@@ -553,6 +591,8 @@
+ ** @param [d] pthys [AjPNexusTaxa*] AjPNexusTaxa object
+ ** @return [void]
+ ** @category delete [AjPNexusTaxa] Default destructor
++**
++** @release 2.8.0
+ ******************************************************************************/
+ 
+ static void nexusTaxaDel(AjPNexusTaxa* pthys)
+@@ -579,6 +619,8 @@
+ ** @param [d] pthys [AjPNexusCharacters*] AjPNexusCharacters object
+ ** @return [void]
+ ** @category delete [AjPNexusCharacters] Default destructor
++**
++** @release 2.8.0
+ ******************************************************************************/
+ 
+ static void nexusCharactersDel(AjPNexusCharacters* pthys)
+@@ -618,6 +660,8 @@
+ ** @param [d] pthys [AjPNexusUnaligned*] AjPNexusUnaligned object
+ ** @return [void]
+ ** @category delete [AjPNexusUnaligned] Default destructor
++**
++** @release 2.8.0
+ ******************************************************************************/
+ 
+ static void nexusUnalignedDel(AjPNexusUnaligned* pthys)
+@@ -650,6 +694,8 @@
+ ** @param [d] pthys [AjPNexusDistances*] AjPNexusDistances object
+ ** @return [void]
+ ** @category delete [AjPNexusDistances] Default destructor
++**
++** @release 2.8.0
+ ******************************************************************************/
+ 
+ static void nexusDistancesDel(AjPNexusDistances* pthys)
+@@ -680,6 +726,8 @@
+ ** @param [d] pthys [AjPNexusSets*] AjPNexusSets object
+ ** @return [void]
+ ** @category delete [AjPNexusSets] Default destructor
++**
++** @release 2.8.0
+ ******************************************************************************/
+ 
+ static void nexusSetsDel(AjPNexusSets* pthys)
+@@ -715,6 +763,8 @@
+ ** @param [d] pthys [AjPNexusAssumptions*] AjPNexuAssumptionss object
+ ** @return [void]
+ ** @category delete [AjPNexusAssumptions] Default destructor
++**
++** @release 2.9.0
+ ******************************************************************************/
+ 
+ static void nexusAssumptionsDel(AjPNexusAssumptions* pthys)
+@@ -750,6 +800,8 @@
+ ** @param [d] pthys [AjPNexusCodons*] AjPNexusCodons object
+ ** @return [void]
+ ** @category delete [AjPNexusCodons] Default destructor
++**
++** @release 2.8.0
+ ******************************************************************************/
+ 
+ static void nexusCodonsDel(AjPNexusCodons* pthys)
+@@ -780,6 +832,8 @@
+ ** @param [d] pthys [AjPNexusTrees*] AjPNexusTrees object
+ ** @return [void]
+ ** @category delete [AjPNexusTrees] Default destructor
++**
++** @release 2.8.0
+ ******************************************************************************/
+ 
+ static void nexusTreesDel(AjPNexusTrees* pthys)
+@@ -802,13 +856,15 @@
+ 
+ 
+ 
+-/* @funcstatic nexusNotesDel ************************************************
++/* @funcstatic nexusNotesDel **************************************************
+ **
+ ** Destructor for AjPNexusNotes
+ **
+ ** @param [d] pthys [AjPNexusNotes*] AjPNexusNotes object
+ ** @return [void]
+ ** @category delete [AjPNexusNotes] Default destructor
++**
++** @release 2.8.0
+ ******************************************************************************/
+ 
+ static void nexusNotesDel(AjPNexusNotes* pthys)
+@@ -841,6 +897,8 @@
+ ** @param [w] list [AjPList] List of block records
+ ** @param [r] blockname [const AjPStr] Block name
+ ** @return [AjBool] ajTrue on success
++**
++** @release 2.8.0
+ ******************************************************************************/
+ 
+ static AjBool nexusBlockSave(AjPNexus thys, AjPList list,
+@@ -905,7 +963,7 @@
+ 
+ 
+ 
+-/* @funcstatic nexusCommand ********************************************
++/* @funcstatic nexusCommand ***************************************************
+ **
+ ** Finds the next command and command string in a block
+ **
+@@ -913,6 +971,8 @@
+ ** @param [w] command [AjPStr*] Command name
+ ** @param [w] cmdstr [AjPStr*] Command string
+ ** @return [AjBool] ajTrue on success
++**
++** @release 2.8.0
+ ******************************************************************************/
+ 
+ static AjBool nexusCommand(AjPList list, AjPStr* command, AjPStr* cmdstr)
+@@ -944,6 +1004,8 @@
+ 		{
+ 		    ajRegPre(endcommand, &tmpstr);
+ 		    ajStrAssignS(cmdstr, tmpstr);
++                    ajStrDel(&tmpstr);
++                    ajStrDel(&rdline);
+ 
+ 		    return ajTrue;
+ 		}
+@@ -957,6 +1019,8 @@
+ 	    {
+ 		ajRegPre(endcommand, &tmpstr);
+ 		ajStrAppendS(cmdstr, tmpstr);
++                ajStrDel(&tmpstr);
++                ajStrDel(&rdline);
+ 
+ 		return ajTrue;
+ 	    }
+@@ -970,19 +1034,23 @@
+ 	}
+     }
+ 
++    ajStrDel(&rdline);
++
+     return ajFalse;
+ }
+ 
+ 
+ 
+ 
+-/* @funcstatic nexusParseTaxa ********************************************
++/* @funcstatic nexusParseTaxa *************************************************
+ **
+ ** Parses Nexus commands for a Taxa block
+ **
+ ** @param [w] thys [AjPNexus] Nexus object
+ ** @param [u] list [AjPList] List of block records
+ ** @return [AjBool] ajTrue on success
++**
++** @release 2.8.0
+ ******************************************************************************/
+ 
+ static AjBool nexusParseTaxa(AjPNexus thys, AjPList list)
+@@ -1024,6 +1092,8 @@
+ 	    if (!thys->Taxa->Ntax)
+ 	    {
+ 		ajDebug("nexusParseTaxa failed: dimension Ntax not found\n");
++                ajStrDel(&command);
++                ajStrDel(&cmdstr);
+ 
+ 		return ajFalse;
+ 	    }
+@@ -1034,12 +1104,17 @@
+ 	    {
+ 		ajDebug("nexusParseTaxa failed: Ntax %d read %d TaxLabels\n",
+ 			thys->Taxa->Ntax, i);
++                ajStrDel(&command);
++                ajStrDel(&cmdstr);
+ 
+ 		return ajFalse;
+ 	    }
+ 	}
+     }
+ 
++    ajStrDel(&command);
++    ajStrDel(&cmdstr);
++
+     if (!thys->Taxa->Ntax)
+     {
+ 	ajDebug("nexusParseTaxa failed: taxa data not found\n");
+@@ -1061,6 +1136,8 @@
+ ** @param [u] list [AjPList] List of block records
+ ** @param [r] newtaxa [AjBool] If true, set NewTaxa
+ ** @return [AjBool] ajTrue on success
++**
++** @release 2.8.0
+ ******************************************************************************/
+ 
+ static AjBool nexusParseCharacters(AjPNexus thys, AjPList list, AjBool newtaxa)
+@@ -1145,6 +1222,8 @@
+ 	    if(!nexusGetInt(cmdstr, dimexp3, 1, &thys->Characters->Nchar))
+ 	    {
+ 		ajDebug("nexusParseCharacters failed: nchar undefined\n");
++                ajStrDel(&command);
++                ajStrDel(&cmdstr);
+ 		return ajFalse;
+ 	    }
+ 	}
+@@ -1197,6 +1276,8 @@
+ 		ajDebug("nexusParseCharacters "
+ 			"failed: Ntax %d read %d TaxLabels\n",
+ 			thys->Taxa->Ntax, i);
++                ajStrDel(&command);
++                ajStrDel(&cmdstr);
+ 
+ 		return ajFalse;
+ 	    }
+@@ -1238,6 +1319,9 @@
+ 	}
+     }
+ 
++    ajStrDel(&command);
++    ajStrDel(&cmdstr);
++
+     if (!thys->Characters->Nchar)
+     {
+ 	ajDebug("nexusParseCharacters failed: dimension nchar undefined\n");
+@@ -1258,6 +1342,8 @@
+ ** @param [w] thys [AjPNexus] Nexus object
+ ** @param [u] list [AjPList] List of block records
+ ** @return [AjBool] ajTrue on success
++**
++** @release 2.8.0
+ ******************************************************************************/
+ 
+ static AjBool nexusParseUnaligned(AjPNexus thys, AjPList list)
+@@ -1336,6 +1422,9 @@
+ 	}
+     }
+ 
++    ajStrDel(&command);
++    ajStrDel(&cmdstr);
++
+     return ajTrue;
+ }
+ 
+@@ -1349,6 +1438,8 @@
+ ** @param [w] thys [AjPNexus] Nexus object
+ ** @param [u] list [AjPList] List of block records
+ ** @return [AjBool] ajTrue on success
++**
++** @release 2.8.0
+ ******************************************************************************/
+ 
+ static AjBool nexusParseDistances(AjPNexus thys, AjPList list)
+@@ -1447,19 +1538,24 @@
+ 	}
+     }
+ 
++    ajStrDel(&command);
++    ajStrDel(&cmdstr);
++
+     return ajTrue;
+ }
+ 
+ 
+ 
+ 
+-/* @funcstatic nexusParseSets ********************************************
++/* @funcstatic nexusParseSets *************************************************
+ **
+ ** Parses Nexus commands for a Sets block
+ **
+ ** @param [w] thys [AjPNexus] Nexus object
+ ** @param [u] list [AjPList] List of block records
+ ** @return [AjBool] ajTrue on success
++**
++** @release 2.8.0
+ ******************************************************************************/
+ 
+ static AjBool nexusParseSets(AjPNexus thys, AjPList list)
+@@ -1505,6 +1601,9 @@
+ 	}
+     }
+ 
++    ajStrDel(&command);
++    ajStrDel(&cmdstr);
++
+     return ajTrue;
+ }
+ 
+@@ -1518,6 +1617,8 @@
+ ** @param [w] thys [AjPNexus] Nexus object
+ ** @param [u] list [AjPList] List of block records
+ ** @return [AjBool] ajTrue on success
++**
++** @release 2.8.0
+ ******************************************************************************/
+ 
+ static AjBool nexusParseAssumptions(AjPNexus thys, AjPList list)
+@@ -1594,19 +1695,24 @@
+ 	}
+     }
+ 
++    ajStrDel(&command);
++    ajStrDel(&cmdstr);
++
+     return ajTrue;
+ }
+ 
+ 
+ 
+ 
+-/* @funcstatic nexusParseCodons ********************************************
++/* @funcstatic nexusParseCodons ***********************************************
+ **
+ ** Parses Nexus commands for a Codons block
+ **
+ ** @param [w] thys [AjPNexus] Nexus object
+ ** @param [u] list [AjPList] List of block records
+ ** @return [AjBool] ajTrue on success
++**
++** @release 2.8.0
+ ******************************************************************************/
+ 
+ static AjBool nexusParseCodons(AjPNexus thys, AjPList list)
+@@ -1640,19 +1746,24 @@
+ 	}
+     }
+ 
++    ajStrDel(&command);
++    ajStrDel(&cmdstr);
++
+     return ajTrue;
+ }
+ 
+ 
+ 
+ 
+-/* @funcstatic nexusParseTrees ********************************************
++/* @funcstatic nexusParseTrees ************************************************
+ **
+ ** Parses Nexus commands for a Trees block
+ **
+ ** @param [w] thys [AjPNexus] Nexus object
+ ** @param [u] list [AjPList] List of block records
+ ** @return [AjBool] ajTrue on success
++**
++** @release 2.8.0
+ ******************************************************************************/
+ 
+ static AjBool nexusParseTrees(AjPNexus thys, AjPList list)
+@@ -1681,19 +1792,24 @@
+ 	}
+     }
+ 
++    ajStrDel(&command);
++    ajStrDel(&cmdstr);
++
+     return ajTrue;
+ }
+ 
+ 
+ 
+ 
+-/* @funcstatic nexusParseNotes ********************************************
++/* @funcstatic nexusParseNotes ************************************************
+ **
+ ** Parses Nexus commands for a Notes block
+ **
+ ** @param [w] thys [AjPNexus] Nexus object
+ ** @param [u] list [AjPList] List of block records
+ ** @return [AjBool] ajTrue on success
++**
++** @release 2.8.0
+ ******************************************************************************/
+ 
+ static AjBool nexusParseNotes(AjPNexus thys, AjPList list)
+@@ -1722,6 +1838,9 @@
+ 	}
+     }
+ 
++    ajStrDel(&command);
++    ajStrDel(&cmdstr);
++
+     return ajTrue;
+ }
+ 
+@@ -1737,6 +1856,8 @@
+ ** @param [u] exp [AjPRegexp] Compiled regular expression for parsing
+ ** @param [w] dest [AjPStr**] Array generated
+ ** @return [ajint] Number of strings returned
++**
++** @release 2.8.0
+ ******************************************************************************/
+ 
+ static ajint nexusGetArray(AjPStr src, AjPRegexp exp,
+@@ -1779,6 +1900,8 @@
+ ** @param [r] isub [ajint] Substring number to extract
+ ** @param [w] dest [AjPStr*] String generated
+ ** @return [AjBool] ajTrue on success
++**
++** @release 2.8.0
+ ******************************************************************************/
+ 
+ static AjBool nexusGetStr(AjPStr src, AjPRegexp exp, ajint isub, AjPStr* dest)
+@@ -1805,6 +1928,8 @@
+ ** @param [r] isub [ajint] Substring number to extract
+ ** @param [w] dest [char*] String generated
+ ** @return [AjBool] ajTrue on success
++**
++** @release 2.8.0
+ ******************************************************************************/
+ 
+ static AjBool nexusGetChar(AjPStr src, AjPRegexp exp, ajint isub, char* dest)
+@@ -1841,6 +1966,8 @@
+ ** @param [r] isub [ajint] Substring number to extract
+ ** @param [w] dest [ajuint*] Integer generated
+ ** @return [AjBool] ajTrue on success
++**
++** @release 2.8.0
+ ******************************************************************************/
+ 
+ static AjBool nexusGetInt(AjPStr src, AjPRegexp exp, ajint isub, ajuint* dest)
+@@ -1860,7 +1987,7 @@
+ 
+ 
+ 
+-/* @funcstatic nexusGetBool **************************************************
++/* @funcstatic nexusGetBool ***************************************************
+ **
+ ** Sets a nexus bool from a parsed nexus command in the form [no]name.
+ ** We know name is found, we test for the "no" part.
+@@ -1870,6 +1997,8 @@
+ ** @param [r] isub [ajint] Substring number to extract
+ ** @param [w] dest [AjBool*] Boolean generated
+ ** @return [AjBool] ajTrue on success
++**
++** @release 2.8.0
+ ******************************************************************************/
+ 
+ static AjBool nexusGetBool(AjPStr src, AjPRegexp exp, ajint isub, AjBool* dest)
+@@ -1893,7 +2022,7 @@
+ 
+ 
+ 
+-/* @funcstatic nexusVocab ***************************************************
++/* @funcstatic nexusVocab *****************************************************
+ **
+ ** Tests a string against a controlled vocabulary
+ **
+@@ -1901,6 +2030,8 @@
+ ** @param [r] src [const AjPStr] String to be tested
+ ** @param [r] vocab [const char* []] List of known values, ending in a NULL
+ ** @return [AjBool] ajTrue on success
++**
++** @release 2.8.0
+ ******************************************************************************/
+ 
+ static AjBool nexusVocab(const char* title, const AjPStr src,
+@@ -1927,6 +2058,8 @@
+ **
+ ** @param [r] thys [const AjPNexus] nexus object
+ ** @return [void]
++**
++** @release 2.8.0
+ ******************************************************************************/
+ 
+ void ajNexusTrace(const AjPNexus thys)
+@@ -2430,6 +2563,8 @@
+ **
+ ** @param [r] thys [const AjPNexus] Nexus object
+ ** @return [AjPStr*] taxa string array, NULL terminated, read only
++**
++** @release 2.8.0
+ ******************************************************************************/
+ 
+ AjPStr* ajNexusGetTaxa(const AjPNexus thys)
+@@ -2452,6 +2587,8 @@
+ **
+ ** @param [r] thys [const AjPNexus] Nexus object
+ ** @return [ajuint] Number of taxa
++**
++** @release 2.8.0
+ ** @@
+ ******************************************************************************/
+ 
+@@ -2478,6 +2615,8 @@
+ **
+ ** @param [u] thys [AjPNexus] Nexus object
+ ** @return [AjPStr*] taxa string array, NULL terminated, read only
++**
++** @release 2.8.0
+ ******************************************************************************/
+ 
+ AjPStr* ajNexusGetSequences(AjPNexus thys)
+@@ -2502,6 +2641,8 @@
+ **
+ ** @param [u] thys [AjPNexus] Nexus object
+ ** @return [AjBool] ajTrue on success
++**
++** @release 2.8.0
+ ******************************************************************************/
+ 
+ static AjBool nexusSetSequences(AjPNexus thys)
+@@ -2591,7 +2732,7 @@
+ 
+ 	for (i=0; thys->Taxa->TaxLabels[i]; i++)
+ 	{
+-	    seqstr = ajStrNewRes(thys->Characters->Nchar+1);
++            seqstr = ajStrNewRes(thys->Characters->Nchar+1);
+ 	    ajTablePut(seqtab, thys->Taxa->TaxLabels[i], seqstr);
+ 	    seqstr = NULL;
+ 	}
+@@ -2599,6 +2740,7 @@
+     else
+     {
+ 	AJCNEW0(thys->Taxa->TaxLabels, (thys->Ntax+1));
++        ajDebug("thys->Taxa->TaxLabels 0..%u\n", (thys->Ntax+1));
+     }
+ 
+     taxlabel = NULL;
+@@ -2609,6 +2751,7 @@
+ 	ajStrAssignS(&rdline, thys->Characters->Matrix[i]);
+ 	ajStrRemoveWhiteExcess(&rdline);
+ 
++        ajDebug("rdline: '%S'\n", rdline);
+ 	if (!taxlabel || thys->Characters->Interleave ||
+ 	    (ajStrGetLen(seqstr) >= thys->Characters->Nchar))
+ 	{				/* next tax label */
+@@ -2617,13 +2760,23 @@
+ 
+ 	    ajRegSubI(word, 0, &taxlabel);
+ 	    ajRegPost(word, &tmpstr);
++            ajDebug("taxlabel '%S' rest '%S'\n", taxlabel, tmpstr);
+ 	    ajStrAssignS(&rdline, tmpstr);
+ 	    ajStrQuoteStripAll(&taxlabel);
++            ajDebug("unquoted taxlabel %p '%S'\n", taxlabel, taxlabel);
+ 
+ 	    if (!havetaxa)
+ 	    {
++                ajDebug("ajTablePut itax.%u label %p '%S'\n",
++                        itax,
++                        thys->Taxa->TaxLabels[itax],
++                        thys->Taxa->TaxLabels[itax]);
+ 		ajStrAssignS(&thys->Taxa->TaxLabels[itax], taxlabel);
+ 		seqstr = ajStrNewRes(thys->Characters->Nchar+1);
++                ajDebug("ajTablePut itax %u label %p '%S'\n",
++                        itax,
++                        thys->Taxa->TaxLabels[itax],
++                        thys->Taxa->TaxLabels[itax]);
+ 		ajTablePut(seqtab, thys->Taxa->TaxLabels[itax], seqstr);
+ 		seqstr = NULL;
+ 		itax++;
+@@ -2631,8 +2784,10 @@
+ 		    havetaxa = ajTrue;
+ 	    }
+ 
++            ajDebug("havetaxa: %B taxlabel '%S'\n", havetaxa, taxlabel);
+ 	    seqstr = ajTableFetchmodS(seqtab, taxlabel);
+ 
++            ajDebug("seqstr '%S'\n", seqstr);
+ 	    if (!seqstr)
+ 	    {
+ 		ajErr("Unknown taxon '%S' in nexus data", taxlabel);
+@@ -2650,12 +2805,12 @@
+ 	{
+ 	    ajRegSubI(word, 0, &tmpstr);
+ 	    ajStrAppendS(&seqstr, tmpstr);
+-	    ajTablePut(seqtab, taxlabel, seqstr); /* just to make sure */
+ 	    ajRegPost(word, &tmpstr);
+ 	    ajStrAssignS(&rdline, tmpstr);
+ 	}
+ 
+ 	ajStrExchangeKK(&seqstr, gapch, '-');
++        ajDebug("seqstr updated '%S'\n", seqstr);
+     }
+ 
+     ajRegFree(&word);
+@@ -2683,6 +2838,8 @@
+     }
+ 
+     ajTableFree(&seqtab);
++    ajStrDel(&firstseq);
++    ajStrDel(&taxlabel);
+ 
+     return ajTrue;
+ }
+@@ -2700,6 +2857,8 @@
+ ** @param  [d] pthis [AjPStr**] Pointer to the string array to be deleted.
+ **         The pointer is always deleted.
+ ** @return [void]
++**
++** @release 4.0.0
+ ** @@
+ ******************************************************************************/
+ 
+--- emboss-6.4.0.orig/ajax/core/ajpat.c
++++ emboss-6.4.0/ajax/core/ajpat.c
+@@ -752,6 +752,8 @@
+ 	default:
+ 	    mismreg = ajRegCompC("<mismatch=(\\d+)>");
+ 
++            mismatch=mismatches; /* set for first pattern */
++
+ 	    while (ajBuffreadLineTrim(infile,&line))
+ 	    {
+ 		if (ajStrGetCharFirst(line) == '>')
+@@ -762,7 +764,7 @@
+ 					    mismatch);
+ 			ajStrSetClear(&name);
+ 			ajStrSetClear(&pat);
+-			mismatch=mismatches;
++			mismatch=mismatches; /* reset for next pattern */
+ 		    }
+ 
+ 		    ajStrCutStart(&line,1);
+--- emboss-6.4.0.orig/ajax/core/ajquery.c
++++ emboss-6.4.0/ajax/core/ajquery.c
+@@ -1609,7 +1609,14 @@
+     fmtstat = ajRegExec(queryRegFmt, *Pqry);
+ 
+     if(!fmtstat)
++    {
++        if(ajStrGetLen(textin->Formatstr))
++        {
++            if(findformat(textin->Formatstr, &textin->Format))
++                ajStrAssignS(&qry->Formatstr, textin->Formatstr);
++        }
+ 	return NULL;
++    }
+ 
+     ajRegSubI(queryRegFmt, 1, &queryFormat);
+     ajRegSubI(queryRegFmt, 2, Pqry);
+@@ -2716,15 +2723,21 @@
+                         ajDebug("ajQueryAddFieldOrC.i '%s' '%S'\n",
+                                 "id", qrystring);
+ 
+-                        ajQueryAddFieldElseC(qry, "acc",
+-                                             MAJSTRGETPTR(qrystring));
+-                        ajDebug("ajQueryAddFieldElseC.i '%s' '%S'\n",
+-                                "acc", qrystring);
++                        if(qry->HasAcc && ajQueryKnownFieldC(qry, "acc"))
++                        {
++                            ajQueryAddFieldElseC(qry, "acc",
++                                                 MAJSTRGETPTR(qrystring));
++                            ajDebug("ajQueryAddFieldElseC.i '%s' '%S'\n",
++                                    "acc", qrystring);
++                        }
+                         
+-                        ajQueryAddFieldElseC(qry, "sv",
+-                                             MAJSTRGETPTR(qrystring));
+-                        ajDebug("ajQueryAddFieldElseC.i '%s' '%S'\n",
+-                                "sv", qrystring);
++                        if(ajQueryKnownFieldC(qry, "sv"))
++                        {
++                            ajQueryAddFieldElseC(qry, "sv",
++                                                 MAJSTRGETPTR(qrystring));
++                            ajDebug("ajQueryAddFieldElseC.i '%s' '%S'\n",
++                                    "sv", qrystring);
++                        }
+                     }
+                     ajStrAssignS(&lastoper, operstr);
+                     ajStrTrimWhite(&lastoper);
+--- emboss-6.4.0.orig/ajax/core/ajrange.c
++++ emboss-6.4.0/ajax/core/ajrange.c
+@@ -179,7 +179,7 @@
+                                   ajuint minsize, ajuint size)
+ {
+     AjPRange ret = NULL;
+-    AjPFile infile;
++    AjPFile infile = NULL;
+     AjPStr line   = NULL;
+     char whiteSpace[] = " \t\n\r";
+     char notSpace[]   = "\n\r";
+@@ -189,9 +189,9 @@
+     ajuint numone;
+     ajuint numtwo;
+     
+-    AjPStr one;
+-    AjPStr two;
+-    AjPStr text;
++    AjPStr one = NULL;
++    AjPStr two = NULL;
++    AjPStr text = NULL;
+     
+     AjPList onelist;
+     AjPList twolist;
+@@ -229,13 +229,17 @@
+ 	one = ajStrNew();
+ 	ajStrTokenNextParse(&tokens, &one);
+ 	ajListstrPushAppend(onelist, one);
++        one = NULL;
+ 	
+ 	two = ajStrNew();
+ 	ajStrTokenNextParse(&tokens, &two);
+ 
+ 	if(ajStrGetLen(two))
+-	    ajListstrPushAppend(twolist, two);
+-	else
++	{
++            ajListstrPushAppend(twolist, two);
++            two = NULL;
++        }
++        else
+ 	{
+ 	    ajWarn("Odd integer(s) in range specification:\n%S\n", line);
+ 
+@@ -247,10 +251,14 @@
+ 	ajStrTokenNextParseC(&tokens, notSpace, &text);
+ 	ajStrTrimWhite(&text);
+ 	ajListstrPushAppend(textlist, text);
++	text = NULL;
+ 	
+ 	ajStrTokenDel( &tokens);	
+     }
+     
++    ajFileClose(&infile);
++    ajStrDel(&line);
++
+     /* now we know how many pairs of numbers to store, create ajRange object */
+     n  = ajListstrGetLength(onelist);
+     if(size)
+@@ -331,6 +339,7 @@
+ 	/* do the text */
+ 	ajListstrPop(textlist, &text);
+ 	ret->text[k] = text;
++        text = NULL;
+     }
+ 
+ 
+--- emboss-6.4.0.orig/ajax/core/ajseqabi.c
++++ emboss-6.4.0/ajax/core/ajseqabi.c
+@@ -181,6 +181,7 @@
+ 	    *machine = ajStrNewRes(l+1);
+ 	    ajReadbinBinary(fp,1,l,(void*)ajStrGetuniquePtr(machine));
+ 	    *(ajStrGetuniquePtr(machine)+l)='\0';
++            ajStrSetValid(machine);
+ 	}
+ 	else
+ 	    return ajFalse;
+@@ -961,6 +962,7 @@
+ 	*sample = ajStrNewRes(l+1);
+ 	ajReadbinBinary(fp,1,l,(void*)ajStrGetuniquePtr(sample));
+ 	*(ajStrGetuniquePtr(sample)+l)='\0';
++        ajStrSetValid(sample);
+     }
+ 
+     return ajTrue;
+--- emboss-6.4.0.orig/ajax/core/ajseqread.c
++++ emboss-6.4.0/ajax/core/ajseqread.c
+@@ -5497,6 +5497,7 @@
+ static AjBool seqReadRaw(AjPSeq thys, AjPSeqin seqin)
+ {
+     AjPFilebuff buff;
++    const char* cp;
+     AjPFile fp;
+     AjBool ok = ajFalse;
+     ajulong filestat = 0L;
+@@ -5506,83 +5507,139 @@
+     AjPStr buf = NULL;
+     char *cbuf;
+     AjPStr tmpseq = NULL;
+-
+-    if(!seqRegRawNonseq)
+-	seqRegRawNonseq = ajRegCompC("[^A-Za-z0-9 \t\n\r*-]");
++    size_t iread;
++    
++    ajDebug("seqReadRaw\n");
+ 
+     buff = seqin->Input->Filebuff;
+     fp = ajFilebuffGetFile(buff);
+ 
+-    ajDebug("seqReadRaw\n");
++    if(!seqRegRawNonseq)
++	seqRegRawNonseq = ajRegCompC("[^A-Za-z0-9 \t\n\r*-]");
+ 
+     if(ajFilebuffIsEnded(buff))
+ 	return ajFalse;
+ 
+-    buf = ajStrNewRes(4096);
+-    ajStrSetValidLen(&buf, inc);
+-    cbuf = ajStrGetuniquePtr(&buf);
+-
+-    filestat = ajFileSeek(fp, 0L, SEEK_END);
+-    filesize = ajFileResetPos(fp);
+-    filestat = ajFileSeek(fp, (ajlong) filestat, 0);
++    filestat = ajFileSeek(fp, 0L, SEEK_CUR);
+ 
+-    ok = ajTrue;
++    if(filestat)
++    {
++        /* not a file - cannot use binary, so we can only read the buffer */
++        while(ajBuffreadLineStore(buff, &seqReadLine,
++                                  seqin->Input->Text, &thys->TextPtr))
++        {
++            ajDebug("read '%S'\n", seqReadLine);
+ 
+-    for(i=0; i < filesize; i += inc)
++            cp = ajStrGetPtr(seqReadLine);
++            if(strlen(cp) != ajStrGetLen(seqReadLine))
++            {
++                ajDebug("seqReadRaw: Null character found in line: %S\n",
++                        seqReadLine);
++                ajFilebuffResetStore(buff, seqin->Input->Text, &thys->TextPtr);
++                ajStrAssignClear(&thys->Seq);
++
++                return ajFalse;
++            }
++        
++            if(ajRegExec(seqRegRawNonseq, seqReadLine))
++            {
++                ajDebug("seqReadRaw: Bad character found in line: %S\n",
++                        seqReadLine);
++                ajFilebuffResetStore(buff, seqin->Input->Text, &thys->TextPtr);
++                ajStrAssignClear(&thys->Seq);
++
++                return ajFalse;
++            }
++            seqAppend(&thys->Seq, seqReadLine);
++            seqin->Input->Records++;
++            ajDebug("read %d lines\n", seqin->Input->Records);
++        }
++    }
++    else
+     {
+-        if((i+inc) > filesize)
++        if(ajFilebuffIsEnded(buff))
+         {
+-	  inc = (ajuint) (filesize - i);
+-            ajStrSetValidLen(&buf, inc);
++            ajFileSeek(fp, 0L, SEEK_END);
++            return ajFalse;
+         }
+ 
+-        ajReadbinBinary(fp, inc, 1, cbuf);
+-        cbuf[inc] = '\0';
++        buf = ajStrNewRes(4096);
++        ajStrSetValidLen(&buf, inc);
++        cbuf = ajStrGetuniquePtr(&buf);
++
++        filestat = ajFileSeek(fp, 0L, SEEK_END);
++        filesize = ajFileResetPos(fp);
++        filestat = ajFileSeek(fp, 0L, SEEK_SET);
+ 
+-        if(strlen(cbuf) != inc)
++        if(!filesize)
+         {
+-	    ajDebug("seqReadRaw: Null character found in line: %s\n",
+-		    cbuf);
+-            ok = ajFalse;
+-            break;
++            ajFileSeek(fp,(ajlong) filesize, SEEK_SET);
++            return ajFalse;
+         }
++        
++        ok = ajTrue;
+ 
+-	if(ajRegExec(seqRegRawNonseq, buf))
+-	{
+-	    ajDebug("seqReadRaw: Bad character found in line: %s\n",
+-		    cbuf);
+-            ok = ajFalse;
+-            break;
+-        }
++        for(i=0; i < filesize; i += inc)
++        {
++            if((i+inc) > filesize)
++            {
++                inc = (ajuint) (filesize - i);
++                ajStrSetValidLen(&buf, inc);
++            }
+ 
+-        ajStrAssignC(&tmpseq, cbuf);
++            iread = ajReadbinBinary(fp, inc, 1, cbuf);
++            cbuf[inc] = '\0';
+ 
+-        if(seqin->Input->Text)
+-            ajStrAppendS(&thys->TextPtr, tmpseq);
++            if(strlen(cbuf) != iread)
++            {
++                ajDebug("seqReadRaw: Null character found in line: %s\n",
++                        cbuf);
++                ok = ajFalse;
++                break;
++            }
+ 
+-	seqAppend(&thys->Seq, tmpseq);
+-	seqin->Input->Records++;
+-        ajDebug("read %d lines\n", seqin->Input->Records);
+-    }
++            if(ajRegExec(seqRegRawNonseq, buf))
++            {
++                ajDebug("seqReadRaw: Bad character found in line: %S\n",
++                        seqReadLine);
++                ok = ajFalse;
++                break;
++            }
+ 
+-    ajStrDel(&buf);
+-    ajStrDel(&tmpseq);
++            ajStrAssignC(&tmpseq, cbuf);
+ 
+-    if(!ok)
+-    {
+-        ajFileSeek(fp,(ajlong) filestat,0);
++            if(seqin->Input->Text)
++                ajStrAppendS(&thys->TextPtr, tmpseq);
++
++            seqAppend(&thys->Seq, tmpseq);
++            seqin->Input->Records++;
++            ajDebug("read %d lines\n", seqin->Input->Records);
++        }
+ 
+-        if(seqin->Input->Text)
+-            ajStrAssignC(&thys->TextPtr, "");
++        ajStrDel(&buf);
++        ajStrDel(&tmpseq);
++
++        if(!ok)
++        {
++            ajFileSeek(fp,(ajlong) filestat,0);
++
++            if(seqin->Input->Text)
++                ajStrAssignC(&thys->TextPtr, "");
++
++            ajFilebuffResetPos(buff);
++
++            return ajFalse;
++        }
+ 
+-	ajFilebuffResetPos(buff);
+ 
+-	return ajFalse;
+     }
+ 
+     ajFilebuffClear(buff, -1);
+     buff->File->End=ajTrue;
+ 
++    if(!seqin->Input->Records)
++	return ajFalse;
++
+     return ajTrue;
+ }
+ 
+@@ -7898,6 +7955,7 @@
+     ajuint j;
+     AjPFilebuff buff;
+     AjPStr* seqs = NULL;
++    AjPStr* names = NULL;
+     AjPNexus nexus = NULL;
+ 
+     SeqPMsfData phydata      = NULL;
+@@ -7953,8 +8011,11 @@
+ 	seqs = ajNexusGetTaxa(phydata->Nexus);
+ 	phydata->Names = AJCALLOC(phydata->Nseq, sizeof(*phydata->Names));
+ 
+-	for(j=0;j<phydata->Nseq;j++)
+-	    ajStrAssignS(&phydata->Names[j], seqs[j]);
++        if(seqs)
++        {
++            for(j=0;j<phydata->Nseq;j++)
++                ajStrAssignS(&phydata->Names[j], seqs[j]);
++        }
+ 
+ 	seqin->SeqData = phydata;
+ 	ajDebug("Nexus parsed %d sequences\n", phydata->Nseq);
+@@ -7974,22 +8035,23 @@
+ 	return ajFalse;
+     }
+ 
+-    if (!phydata->Names)		/* finally set from the sequences */
+-    {
+-	seqs = ajNexusGetTaxa(phydata->Nexus);
++    thys->Weight = 1.0;
++    ajStrAssignS(&thys->Seq, seqs[i]);
++
++    if (!phydata->Names)
+ 	phydata->Names = AJCALLOC(phydata->Nseq, sizeof(*phydata->Names));
+ 
++    if (!phydata->Names[0])		/* finally set from the sequences */
++    {
++	names = ajNexusGetTaxa(phydata->Nexus);
+ 	for(j=0;j<phydata->Nseq;j++)
+-	    ajStrAssignS(&phydata->Names[j], seqs[j]);
++	    ajStrAssignS(&phydata->Names[j], names[j]);
+     }
+ 
+     ajDebug("returning [%d] '%S'\n", i, phydata->Names[i]);
+ 
+     ajStrAssignS(&thys->Name, phydata->Names[i]);
+ 
+-    thys->Weight = 1.0;
+-    ajStrAssignS(&thys->Seq, seqs[i]);
+-
+     phydata->Count++;
+ 
+     if(phydata->Count >= phydata->Nseq)
+@@ -13827,7 +13889,7 @@
+ 	ajStrAssignC(&seqFtFmtGff, "gff3");
+ 
+     if(!seqRegGff3Typ)
+-	seqRegGff3Typ = ajRegCompC("^#!(.*)");
++	seqRegGff3Typ = ajRegCompC("^#!Type (.*)");
+ 
+     ok = ajBuffreadLineStore(buff, &seqReadLine,
+ 			    seqin->Input->Text, &thys->TextPtr);
+@@ -13885,7 +13947,8 @@
+ 
+ 	if(ajRegExec(seqRegGff3Typ, seqReadLine))
+ 	{
+-	    ajFmtPrintS(&outstr, "%S\n", seqReadLine);
++ 	    ajRegSubI(seqRegGff3Typ, 1, &typstr);
++ 	    ajFmtPrintS(&outstr, "#!Type %S", typstr);
+ 	}
+ 
+ 	ok = ajBuffreadLineStore(buff, &seqReadLine,
+@@ -13966,7 +14029,7 @@
+ 	ajFeattabinDel(&seqin->Ftquery);
+ 	seqin->Ftquery = ajFeattabinNewSSF(seqFtFmtGff, thys->Name,
+ 					   ajStrGetPtr(seqin->Type), ftfile);
+-	ajDebug("GFF FEAT TabIn %x\n", seqin->Ftquery);
++	ajDebug("GFF3 FEAT TabIn %x\n", seqin->Ftquery);
+ 	ftfile = NULL;
+ 	ajFeattableDel(&seqin->Fttable);
+ 	ajFeattableDel(&thys->Fttable);
+--- emboss-6.4.0.orig/ajax/ensembl/ensdatabaseadaptor.c
++++ emboss-6.4.0/ajax/ensembl/ensdatabaseadaptor.c
+@@ -156,8 +156,8 @@
+ ** @argrule Ini dbc [EnsPDatabaseconnection] Ensembl Database Connection
+ ** @argrule Ini database [AjPStr] Database name
+ ** @argrule Ini species [AjPStr] Species
+-** @argrule Ini dbag [EnsEDatabaseadaptorGroup] Ensembl Database Adaptor Group
+-** enumeration
++** @argrule Ini dbag [EnsEDatabaseadaptorGroup]
++** Ensembl Database Adaptor Group enumeration
+ ** @argrule Ini multi [AjBool] Multiple species
+ ** @argrule Ini identifier [ajuint] Species identifier
+ ** @argrule Url url [const AjPStr] Uniform Resource Locator
+@@ -239,7 +239,7 @@
+         return NULL;
+ 
+     collectionre =
+-        ajRegCompC("^\\w+_collection_([a-z]+)(?:_\\d+)?_(\\d+)_\\w+");
++        ajRegCompC("^(\\w+)_collection_([a-z]+)(?:_\\d+)?_(\\d+)_\\w+");
+ 
+     multire =
+         ajRegCompC("^ensembl_([a-z]+)(_\\w+?)*?(?:_\\d+)?_(\\d+)$");
+@@ -254,10 +254,12 @@
+         /* Ensembl Collection databases have to be matched first. */
+ 
+         group     = ajStrNew();
++        prefix    = ajStrNew();
+         swversion = ajStrNew();
+ 
+-        ajRegSubI(collectionre, 1, &group);
+-        ajRegSubI(collectionre, 2, &swversion);
++        ajRegSubI(collectionre, 1, &prefix);
++        ajRegSubI(collectionre, 2, &group);
++        ajRegSubI(collectionre, 3, &swversion);
+ 
+         if(ajStrMatchCaseC(swversion, ensSoftwareVersion))
+         {
+@@ -290,6 +292,7 @@
+         }
+ 
+         ajStrDel(&group);
++        ajStrDel(&prefix);
+         ajStrDel(&swversion);
+     }
+     else if(ajRegExec(multire, database))
+@@ -417,6 +420,9 @@
+ **
+ ** Constructor for an Ensembl Database Adaptor with initial values.
+ **
++** If a database name has not been provided, the database name of the
++** Ensembl Database Connection will be used.
++**
+ ** Ensembl Database Adaptors are singleton objects in the sense that a single
+ ** instance of an Ensembl Database Adaptor connected to a particular database
+ ** is sufficient to instantiate any number of Ensembl Object Adaptors from the
+@@ -430,12 +436,10 @@
+ **
+ ** @cc Bio::EnsEMBL::DBSQL::DBAdaptor::new
+ ** @param [u] dbc [EnsPDatabaseconnection] Ensembl Database Connection
+-** @param [u] database [AjPStr] Database name (optional). If not provided, the
+-**                              database name in the Database Connection will
+-**                              be used.
++** @param [uN] database [AjPStr] Database name
+ ** @param [u] species [AjPStr] Species
+-** @param [u] dbag [EnsEDatabaseadaptorGroup] Ensembl Database Adaptor Group
+-** enumeration
++** @param [u] dbag [EnsEDatabaseadaptorGroup]
++** Ensembl Database Adaptor Group enumeration
+ ** @param [r] multi [AjBool] Multiple species
+ ** @param [r] identifier [ajuint] Species identifier
+ **
+@@ -555,15 +559,15 @@
+ 
+ /* @section destructors *******************************************************
+ **
+-** Destruction destroys all internal data structures and frees the
+-** memory allocated for an Ensembl Database Adaptor object.
++** Destruction destroys all internal data structures and frees the memory
++** allocated for an Ensembl Database Adaptor object.
+ **
+ ** @fdata [EnsPDatabaseadaptor]
+ **
+-** @nam3rule Del Destroy (free) an Ensembl Database Adaptor object
++** @nam3rule Del Destroy (free) an Ensembl Database Adaptor
+ **
+-** @argrule * Pdba [EnsPDatabaseadaptor*] Ensembl Database Adaptor
+-**                                        object address
++** @argrule * Pdba [EnsPDatabaseadaptor*]
++** Ensembl Database Adaptor address
+ **
+ ** @valrule * [void]
+ **
+@@ -586,8 +590,7 @@
+ ** @see ensExit
+ ** @see ensRegistryExit
+ **
+-** @param [d] Pdba [EnsPDatabaseadaptor*] Ensembl Database Adaptor
+-**                                        object address
++** @param [d] Pdba [EnsPDatabaseadaptor*] Ensembl Database Adaptor address
+ **
+ ** @return [void]
+ ** @@
+@@ -652,8 +655,8 @@
+ ** @valrule Databaseconnection [EnsPDatabaseconnection]
+ ** Ensembl Database Connection or NULL
+ ** @valrule Species [AjPStr] Species or NULL
+-** @valrule Group [EnsEDatabaseadaptorGroup] Ensembl Database Adaptor Group
+-** enumeration or ensEDatabaseadaptorGroupNULL
++** @valrule Group [EnsEDatabaseadaptorGroup]
++** Ensembl Database Adaptor Group enumeration or ensEDatabaseadaptorGroupNULL
+ ** @valrule Multispecies [AjBool] Multiple species or ajFalse
+ ** @valrule Identifier [ajuint] Species identifier or 0
+ **
+@@ -693,8 +696,8 @@
+ ** @cc Bio::EnsEMBL::DBSQL::DBAdaptor::group
+ ** @param [r] dba [const EnsPDatabaseadaptor] Ensembl Database Adaptor
+ **
+-** @return [EnsEDatabaseadaptorGroup] Ensembl Database Adaptor Group
+-** enumeration or ensEDatabaseadaptorGroupNULL
++** @return [EnsEDatabaseadaptorGroup]
++** Ensembl Database Adaptor Group enumeration or ensEDatabaseadaptorGroupNULL
+ ** @@
+ ******************************************************************************/
+ 
+@@ -793,10 +796,10 @@
+ ** @nam4rule Species Set the species
+ **
+ ** @argrule * dba [EnsPDatabaseadaptor] Ensembl Database Adaptor object
+-** @argrule Databaseconnection dbc [EnsPDatabaseconnection] Ensembl Database
+-** Connection
+-** @argrule Group dbag [EnsEDatabaseadaptorGroup] Ensembl Database Adaptor
+-** Group enumeration
++** @argrule Databaseconnection dbc [EnsPDatabaseconnection]
++** Ensembl Database Connection
++** @argrule Group dbag [EnsEDatabaseadaptorGroup]
++** Ensembl Database Adaptor Group enumeration
+ ** @argrule Identifier identifier [ajuint] Species identifier
+ ** @argrule Multispecies multi [AjBool] Multi-species attribute
+ ** @argrule Species species [AjPStr] Species
+--- emboss-6.4.0.orig/ajax/ensembl/ensdatabaseadaptor.h
++++ emboss-6.4.0/ajax/ensembl/ensdatabaseadaptor.h
+@@ -121,7 +121,7 @@
+ 
+ EnsPDatabaseadaptor ensRegistryGetDatabaseadaptor(
+     EnsEDatabaseadaptorGroup dbag,
+-    const AjPStr alias);
++    AjPStr alias);
+ 
+ EnsPDatabaseadaptor ensRegistryGetReferenceadaptor(EnsPDatabaseadaptor dba);
+ 
+--- emboss-6.4.0.orig/ajax/ensembl/ensregistry.c
++++ emboss-6.4.0/ajax/ensembl/ensregistry.c
+@@ -569,8 +569,6 @@
+     const RegistryPQualityCheck rqc,
+     ajuint level);
+ 
+-static AjPStr registryAliasRegister(const AjPStr alias);
+-
+ static AjBool registryAliasLoadDatabaseconnection(
+     EnsPDatabaseconnection dbc,
+     EnsPDatabaseadaptor dba);
+@@ -2029,6 +2027,8 @@
+ 
+ AjBool ensRegistryLoadServername(AjPStr servername)
+ {
++    ajuint dbid = 0;
++
+     AjBool debug      = AJFALSE;
+     AjBool registered = AJFALSE;
+ 
+@@ -2037,6 +2037,9 @@
+     AjPList svrnames = NULL;
+     AjPList dbnames  = NULL;
+ 
++    AjPRegexp dbidre = NULL;
++
++    AjPStr dbidstr = NULL;
+     AjPStr dbname  = NULL;
+     AjPStr source  = NULL;
+     AjPStr svrname = NULL;
+@@ -2059,6 +2062,8 @@
+     ** List objects must be re-created and freed for each server.
+     */
+ 
++    dbidre = ajRegCompC("SpeciesIdentifier=(\\d+)");
++
+     value = ajStrNew();
+ 
+     svrnames = ajListstrNew();
+@@ -2103,17 +2108,15 @@
+ 
+             registrySourceRegister(source, &registered);
+ 
++            if((debug == ajTrue) && (registered == ajTrue))
++                ajDebug("ensRegistryLoadServername '%S' already "
++                        "registered via source '%S'.\n",
++                        svrname, source);
++
+             ajStrDel(&source);
+ 
+             if(registered == ajTrue)
+-            {
+-                if(debug)
+-                    ajDebug("ensRegistryLoadServername '%S' already "
+-                            "registered.\n",
+-                            svrname);
+-
+                 continue;
+-            }
+ 
+             /*
+             ** Create an Ensembl Database Connection to the AJAX Server for
+@@ -2150,40 +2153,64 @@
+ 
+                 dba = ensDatabaseadaptorNewUrl(value);
+ 
+-                if((ensDatabaseadaptorGetMultispecies(dba) == ajTrue) &&
+-                   (ensDatabaseadaptorGetIdentifier(dba) == 0))
++                if(ensDatabaseadaptorGetMultispecies(dba) == ajTrue)
+                 {
+                     /*
+-                    ** Expand an Ensembl Database Adaptor representing a
+-                    ** collection database into species-specific
+-                    ** Ensembl Database Adaptor objects before registering.
+-                    ** Delete the Ensembl Database Adaptor for the collection.
++                    ** For Ensembl Database Adaptors representing collection
++                    ** databases, the species name needs resetting to the AJAX
++                    ** database name and the species identifier needs parsing
++                    ** from the comment field of the AJAX database definition.
+                     */
+ 
+-                    registryEntryLoadCollection(
+-                        dbc,
+-                        ensDatabaseconnectionGetDatabasename(
+-                            ensDatabaseadaptorGetDatabaseconnection(dba)),
+-                        ensDatabaseadaptorGetGroup(dba));
++                    ensDatabaseadaptorSetSpecies(dba, dbname);
+ 
+-                    ensDatabaseadaptorDel(&dba);
+-                }
+-                else
+-                {
+-                    /*
+-                    ** Register Ensembl Database Adaptor objects for
+-                    ** multi-species and species-specific databases.
+-                    ** Add the species as alias if registered or delete the
+-                    ** Ensembl Database Adaptor if not registered,
+-                    ** successfully.
+-                    */
++                    ajNamSvrGetdbAttrC(svrname, dbname, "comment", &value);
+ 
+-                    if(ensRegistryAddDatabaseadaptor(dba))
+-                        ensRegistryAliasAdd(ensDatabaseadaptorGetSpecies(dba),
+-                                            ensDatabaseadaptorGetSpecies(dba));
++                    if(ajRegExec(dbidre, value))
++                    {
++                        dbid    = 0;
++                        dbidstr = ajStrNew();
++
++                        ajRegSubI(dbidre, 1, &dbidstr);
++
++                        if(ajStrToUint(dbidstr, &dbid))
++                        {
++                            ensDatabaseadaptorSetIdentifier(dba, dbid);
++
++                            ajStrDel(&dbidstr);
++                        }
++                        else
++                        {
++                            ajDebug("ensRegistryLoadServer could not parse a "
++                                    "valid unsigned integer from the "
++                                    "'SpeciesIdentifer=INTEGER' expression in "
++                                    "the comment field of AJAX database "
++                                    "definition for Ensembl collection "
++                                    "database '%S'.\n", dbname);
++
++                            ajStrDel(&dbidstr);
++
++                            ensDatabaseadaptorDel(&dba);
++
++                            continue;
++                        }
++                    }
+                     else
++                    {
++                        ajDebug("ensRegistryLoadServer could not find a "
++                                "'SpeciesIdentifer=INTEGER' entry in the "
++                                "comment field of AJAX database "
++                                "definition for Ensembl collection "
++                                "database '%S'.\n", dbname);
++
+                         ensDatabaseadaptorDel(&dba);
++
++                        continue;
++                    }
+                 }
++
++                if(ensRegistryAddDatabaseadaptor(dba) == ajFalse)
++                    ensDatabaseadaptorDel(&dba);
+             }
+ 
+             ajListIterDel(&dbniter);
+@@ -2196,6 +2223,8 @@
+     ajListIterDel(&svriter);
+     ajListstrFree(&svrnames);
+ 
++    ajRegFree(&dbidre);
++
+     ajStrDel(&value);
+ 
+     if(debug)
+@@ -2370,70 +2399,6 @@
+ 
+ 
+ 
+-/* @funcstatic registryAliasRegister ******************************************
+-**
+-** Check, whether an alias name can be resolved directly or after replacing
+-** underscore characters into a species name. If not, register the alias
+-** without underscore characters and set the alias with underscores as alias.
+-**
+-** @param [r] alias [const AjPStr] Alias name
+-**
+-** @return [AjPStr] Species name or NULL
+-** @@
+-******************************************************************************/
+-
+-static AjPStr registryAliasRegister(const AjPStr alias)
+-{
+-    AjPStr species = NULL;
+-    AjPStr unalias = NULL;
+-
+-    if(!(alias && ajStrGetLen(alias)))
+-        return NULL;
+-
+-    /* Resolve an eventual alias to the species name. */
+-
+-    ensRegistryAliasResolve(alias, &species);
+-
+-    if(!species)
+-    {
+-        /*
+-        ** If this alias has not been registered before, test if it has been
+-        ** registered without underscores.
+-        */
+-
+-        unalias = ajStrNewS(alias);
+-
+-        /*
+-        ** FIXME: Since EMBOSS DBNAMES cannot cope with spaces species names
+-        ** must include underscores.
+-        ajStrExchangeCC(&unalias, "_", " ");
+-        */
+-
+-        ensRegistryAliasResolve(unalias, &species);
+-
+-        if(!species)
+-        {
+-            /*
+-            ** If the alias without underscores has also not been registered
+-            ** before, register it as species before registering the one
+-            ** with underscores as alias.
+-            */
+-
+-            ensRegistryAliasAdd(unalias, unalias);
+-            ensRegistryAliasAdd(unalias, alias);
+-
+-            ensRegistryAliasResolve(alias, &species);
+-        }
+-
+-        ajStrDel(&unalias);
+-    }
+-
+-    return species;
+-}
+-
+-
+-
+-
+ /* @func ensRegistryAliasAdd **************************************************
+ **
+ ** Add a Registry Alias entry to the Ensembl Registry.
+@@ -2861,8 +2826,6 @@
+ 
+             ajStrAssignS(&species, line);
+ 
+-            ensRegistryAliasAdd(species, species);
+-
+             block = ajTrue;
+         }
+     }
+@@ -3387,8 +3350,6 @@
+         ajSqlcolumnToUint(sqlr, &identifier);
+         ajSqlcolumnToStr(sqlr, &species);
+ 
+-        ensRegistryAliasAdd(species, species);
+-
+         dba = ensRegistryNewDatabaseadaptor(dbc,
+                                             dbname,
+                                             species,
+@@ -3699,7 +3660,10 @@
+     if(!alias)
+         return NULL;
+ 
+-    species = registryAliasRegister(alias);
++    ensRegistryAliasResolve(alias, &species);
++
++    if(species == NULL)
++        species = alias;
+ 
+     dba = ensDatabaseadaptorNewIni(dbc,
+                                    database,
+@@ -3801,7 +3765,10 @@
+     if(!alias)
+         return NULL;
+ 
+-    species = registryAliasRegister(alias);
++    ensRegistryAliasResolve(alias, &species);
++
++    if(species == NULL)
++        species = alias;
+ 
+     rsa = ensDatabaseadaptorNewIni(dbc,
+                                    database,
+@@ -4517,13 +4484,13 @@
+ **
+ ** @argrule AllDatabaseadaptors dbag [EnsEDatabaseadaptorGroup]
+ ** Ensembl Database Adaptor Group enumeration
+-** @argrule AllDatabaseadaptors alias [const AjPStr]
++** @argrule AllDatabaseadaptors alias [AjPStr]
+ ** Ensembl Database Adaptor alias name or species name
+ ** @argrule AllDatabaseadaptors dbas [AjPList] AJAX List of
+ ** Ensembl Database Adaptor objects
+ ** @argrule Databaseadaptor dbag [EnsEDatabaseadaptorGroup]
+ ** Ensembl Database Adaptor Group enumeration
+-** @argrule Databaseadaptor alias [const AjPStr]
++** @argrule Databaseadaptor alias [AjPStr]
+ ** Ensembl Database Adaptor alias name or species name
+ ** @argrule Referenceadaptor dba [EnsPDatabaseadaptor] Ensembl Database Adaptor
+ **
+@@ -4549,7 +4516,7 @@
+ **
+ ** @param [uN] dbag [EnsEDatabaseadaptorGroup] Ensembl Database Adaptor Group
+ ** enumeration
+-** @param [rN] alias [const AjPStr] Ensembl Database Adaptor alias name or
++** @param [rN] alias [AjPStr] Ensembl Database Adaptor alias name or
+ ** species name
+ ** @param [u] dbas [AjPList] AJAX List of Ensembl Database Adaptor objects
+ **
+@@ -4558,7 +4525,7 @@
+ ******************************************************************************/
+ 
+ AjBool ensRegistryGetAllDatabaseadaptors(EnsEDatabaseadaptorGroup dbag,
+-                                         const AjPStr alias,
++                                         AjPStr alias,
+                                          AjPList dbas)
+ {
+     void** keyarray = NULL;
+@@ -4593,8 +4560,17 @@
+     if(!dbas)
+         return ajFalse;
+ 
++    /*
++    ** Resolve an alias name into a valid species name. If the alias did not
++    ** resolve into a species name, use the alias directly. If an alias was
++    ** not passed in, it is still NULL, implying all species.
++    */
++
+     ensRegistryAliasResolve(alias, &species);
+ 
++    if(species == NULL)
++        species = alias;
++
+     ajTableToarrayKeysValues(registryEntry, &keyarray, &valarray);
+ 
+     for(i = 0; keyarray[i]; i++)
+@@ -4761,7 +4737,7 @@
+ ** @cc Bio::EnsEMBL::Registry::get_DBAdaptor
+ ** @param [u] dbag [EnsEDatabaseadaptorGroup] Ensembl Database Adaptor Group
+ ** enumeration
+-** @param [r] alias [const AjPStr] Scientific species name or alias name
++** @param [r] alias [AjPStr] Scientific species name or alias name
+ **
+ ** @return [EnsPDatabaseadaptor] Ensembl Database Adaptor or NULL
+ ** @@
+@@ -4769,7 +4745,7 @@
+ 
+ EnsPDatabaseadaptor ensRegistryGetDatabaseadaptor(
+     EnsEDatabaseadaptorGroup dbag,
+-    const AjPStr alias)
++    AjPStr alias)
+ {
+     AjBool debug = AJFALSE;
+ 
+@@ -4797,8 +4773,16 @@
+     if(!alias)
+         return NULL;
+ 
++    /*
++    ** Resolve an alias name into a valid species name. If the alias did not
++    ** resolve into a species name, use the alias directly.
++    */
++
+     ensRegistryAliasResolve(alias, &species);
+ 
++    if(species == NULL)
++        species = alias;
++
+     if(debug)
+         ajDebug("ensRegistryGetDatabaseadaptor alias '%S' -> species '%S'\n",
+                 alias, species);
+--- emboss-6.4.0.orig/ajax/ensembl/ensregistry.h
++++ emboss-6.4.0/ajax/ensembl/ensregistry.h
+@@ -116,7 +116,7 @@
+ AjBool ensRegistryRemoveDatabaseadaptor(EnsPDatabaseadaptor* Pdba);
+ 
+ AjBool ensRegistryGetAllDatabaseadaptors(EnsEDatabaseadaptorGroup dbag,
+-                                         const AjPStr alias,
++                                         AjPStr alias,
+                                          AjPList dbas);
+ 
+ AjPStr ensRegistryGetStableidentifierprefix(EnsPDatabaseadaptor dba);
+--- emboss-6.4.0.orig/emboss/cacheensembl.c
++++ emboss-6.4.0/emboss/cacheensembl.c
+@@ -181,6 +181,11 @@
+                 ajFmtPrintF(outf, "%S\n", dbname);
+ 
+             ajFmtPrintF(cachef, "DBNAME %S [\n", dbname);
++
++            if(ensDatabaseadaptorGetMultispecies(dba) == ajTrue)
++                ajFmtPrintF(cachef, "  comment: \"SpeciesIdentifier=%u\"\n",
++                            ensDatabaseadaptorGetIdentifier(dba));
++
+             ajFmtPrintF(cachef, "  release: \"%s\"\n", ensSoftwareGetVersion());
+             ajFmtPrintF(cachef, "  server:  \"%S\"\n", svrname);
+             ajFmtPrintF(cachef, "  url:     \"%S\"\n", dbcurl);
+--- emboss-6.4.0.orig/emboss/cirdna.c
++++ emboss-6.4.0/emboss/cirdna.c
+@@ -970,7 +970,7 @@
+     {
+ 	token = ajStrParseC(Name2, ";");
+ 	/*ajStrExchangeCC(&Name2, ";", " ");*/
+-	stringLength = ajGraphicsCalcTextlengthS(token);
++	stringLength = mmtolen * ajGraphicsCalcTextlengthS(token);
+ 	xy1 = ajGraphicsCalcCoord(xDraw, yDraw, r2Ticks+postext, Angle);
+ 	xy2 = ajGraphicsCalcCoord(xDraw, yDraw, r2Ticks+postext+stringLength,
+ 			     Angle);
+@@ -1029,6 +1029,10 @@
+     float stringHeight;
+     float r1Blocks;
+     float r2Blocks;
++    float mmtolen;
++
++    /* radius is 2pi*radius in mm, RealLength in bases */
++    mmtolen = RealLength/(Radius * (float) 2.0 * (float) 3.1416);
+ 
+     r1Blocks = Radius+((float)1.0*BlockHeight/(float)2);
+     r2Blocks = r1Blocks-BlockHeight;
+@@ -1053,15 +1057,17 @@
+ 	ajGraphicsSetFgcolour(Colour);
+     }
+ 
+-    stringLength = cirdna_HorTextPileLengthMax(Name2, NumNames);
++    stringLength = mmtolen * cirdna_HorTextPileLengthMax(Name2, NumNames);
+     stringHeight = ajGraphicsCalcTextheight();
+-    StartAngle   = cirdna_ComputeAngle(RealLength, (To+From)/2+stringLength/2,
++    StartAngle   = cirdna_ComputeAngle(RealLength,
++                                       (To+From)/2 + stringLength/2,
+ 				       OriginAngle);
+-    EndAngle = cirdna_ComputeAngle(RealLength, (To+From)/2-stringLength/2,
++    EndAngle = cirdna_ComputeAngle(RealLength,
++                                   (To+From)/2 - stringLength/2,
+ 				   OriginAngle);
+ 
+     if(ajStrMatchCaseC(PosBlocks, "Out") )
+-	cirdna_HorTextPile(xDraw, yDraw, r1Blocks+(Adjust*postext), StartAngle,
++	cirdna_HorTextPile(xDraw, yDraw, r1Blocks+Adjust*postext, StartAngle,
+ 			   EndAngle, Name2, postext, 1);
+     else
+ 	cirdna_HorTextPile(xDraw, yDraw,
+--- emboss-6.4.0.orig/emboss/data/Efeatures.gff3protein
++++ emboss-6.4.0/emboss/data/Efeatures.gff3protein
+@@ -193,7 +193,7 @@
+ 
+ # METAL - Binding site for a metal ion.
+ 
+-metal_binding SO:0001092 SO:0001092_metal
++polypeptide_metal_contact SO:0001092 SO:0001092_metal
+ 	/note
+ 	/comment
+ 
+@@ -215,11 +215,7 @@
+ #                            internal cyclic lactam
+ #SULFATATION                 Generally of tyrosine
+ 
+-protein_modification_categorized_by_chemical_process MOD:01156
+-	/note
+-	/comment
+-
+-post_translational_modification SO:0001089
++post_translationally_modified_region MOD:01156 SO:0001089
+ 	/note
+ 	/comment
+ 
+@@ -351,7 +347,7 @@
+ 
+ # TURN -  DSSP secondary structure
+ 
+-turn SO:0001128
++polypeptide_turn_motif SO:0001128
+ 	/note
+ 	/comment
+ 
+@@ -371,7 +367,7 @@
+ #	/comment
+ 	/ftid
+ 
+-natural_variant SO:0001147 SO:0001147_variant
++natural_variant_site SO:0001147 SO:0001147_variant
+ 	/note
+ 	/comment
+ 	/ftid
+--- emboss-6.4.0.orig/emboss/data/Etcode.dat
++++ emboss-6.4.0/emboss/data/Etcode.dat
+@@ -22,6 +22,7 @@
+ 0.25
+ 0.23
+ 0.21
++0.19
+ 0.17
+ 0.00
+ #
+--- emboss-6.4.0.orig/emboss/dbiflat.c
++++ emboss-6.4.0/emboss/dbiflat.c
+@@ -91,6 +91,10 @@
+ 
+ static AjPList* fdl  = NULL;
+ 
++static AjBool dbiflat_ParseSwiss(AjPFile libr, AjPFile* alistfile,
++                                 AjBool systemsort, AjPStr* fields,
++                                 ajint* maxFieldLen, ajuint* countfield,
++                                 ajint *dpos, AjPStr* myid, AjPList* acl);
+ static AjBool dbiflat_ParseEmbl(AjPFile libr, AjPFile* alistfile,
+ 				AjBool systemsort, AjPStr* fields,
+ 				ajint* maxFieldLen, ajuint* countfield,
+@@ -135,7 +139,7 @@
+ static DbiflatOParser parser[] =
+ {
+     {"EMBL", dbiflat_ParseEmbl},
+-    {"SWISS", dbiflat_ParseEmbl},
++    {"SWISS", dbiflat_ParseSwiss},
+     {"GB", dbiflat_ParseGenbank},
+     {"REFSEQ", dbiflat_ParseRefseq},
+     {NULL, NULL}
+@@ -594,6 +598,385 @@
+ }
+ 
+ 
++
++
++/* @funcstatic dbiflat_ParseSwiss *********************************************
++**
++** Parse the ID, accession from a SwissProt or UniProtKB entry.
++**
++** Reads to the end of the entry and then returns.
++**
++** @param [u] libr [AjPFile] Input database file
++** @param [u] alistfile [AjPFile*] field data files array
++** @param [r] systemsort [AjBool] If ajTrue use system sort, else internal sort
++** @param [w] fields [AjPStr*] Fields required
++** @param [w] maxFieldLen [ajint*] Maximum token length for each field
++** @param [w] countfield [ajuint*] Number of tokens for each field
++** @param [w] dpos [ajint*] Byte offset
++** @param [w] myid [AjPStr*] ID
++** @param [w] myfdl [AjPList*] Lists of field values
++** @return [AjBool] ajTrue on success.
++** @@
++******************************************************************************/
++
++static AjBool dbiflat_ParseSwiss(AjPFile libr, AjPFile* alistfile,
++                                 AjBool systemsort, AjPStr* fields,
++                                 ajint* maxFieldLen, ajuint* countfield,
++                                 ajint* dpos, AjPStr* myid,
++                                 AjPList* myfdl)
++{
++    AjPStr tmpacnum = NULL;
++    char* fd;
++    ajint lineType;
++    static ajint numFields;
++    static ajint accfield = -1;
++    static ajint desfield = -1;
++    static ajint keyfield = -1;
++    static ajint taxfield = -1;
++    static ajint svnfield = -1;
++    static AjBool reset = AJTRUE;
++    AjBool svndone = ajFalse;
++    AjBool done = ajFalse;
++    ajint i;
++    ajint lo;
++    ajint hi;
++    ajint fieldwidth;
++    AjPStr tmpac = NULL;
++    AjPStr format = NULL;
++    AjPStr prefix = NULL;
++    const char* p;
++    const char* q;
++    const char* swissprefix[] = {
++        "RecName: ", "AltName: ", "SubName: ",
++        "Includes:", "Contains:", "Flags: ",
++        "Full=", "Short=", "EC=",
++        "Allergen=", "Biotech=", "CD_antigen=", "INN=",
++        NULL
++    };
++    ajuint j;
++
++    if(!fields)
++    {
++	reset = ajTrue;
++	accfield = svnfield = desfield = keyfield = taxfield = -1;
++	return ajFalse;
++    }
++
++    if(reset)
++    {
++	numFields = 0;
++	while(fields[numFields])
++	{
++	    countfield[numFields]=0;
++	    if(ajStrMatchCaseC(fields[numFields], "acc"))
++		accfield=numFields;
++	    else if(ajStrMatchCaseC(fields[numFields], "sv"))
++		svnfield=numFields;
++	    else if(ajStrMatchCaseC(fields[numFields], "des"))
++		desfield=numFields;
++	    else if(ajStrMatchCaseC(fields[numFields], "key"))
++		keyfield=numFields;
++	    else if(ajStrMatchCaseC(fields[numFields], "org"))
++		taxfield=numFields;
++	    else
++		ajWarn("EMBL parsing unknown field '%S' ignored",
++		       fields[numFields]);
++	    numFields++;
++	}
++
++	reset = ajFalse;
++    }
++
++    if(!regEmblType)
++	regEmblType = ajRegCompC("^([A-Z][A-Z]) +");
++
++    if(!regEmblAcc)
++	regEmblAcc = ajRegCompC("([A-Za-z0-9-]+)");
++
++    if(!regEmblWrd)
++	regEmblWrd = ajRegCompC("([A-Za-z0-9_]+)");
++
++    if(!regEmblVer)
++	regEmblVer = ajRegCompC("([A-Za-z0-9_.]+)");
++
++    if(!regEmblPhr)
++	regEmblPhr = ajRegCompC(" *([^;.\n\r]+)");
++
++    if(!regEmblTax)
++	regEmblTax = ajRegCompC(" *([^;.\n\r()]+)");
++
++    if(!regEmblId)
++	regEmblId = ajRegCompC("^ID   ([^\\s;]+)(;\\s+SV\\s+(\\d+))?");
++
++    if(!regEmblEnd)
++	regEmblEnd = ajRegCompC("^//");
++
++    *dpos = (ajint) ajFileResetPos(libr); /* Lossy cast */
++
++    while(ajReadline(libr, &rline))
++    {
++	if(ajRegExec(regEmblEnd, rline))
++	{
++	    done = ajTrue;
++	    break;
++	}
++
++	if(ajRegExec(regEmblType, rline))
++	{
++	    ajRegSubI(regEmblType, 1, &typStr);
++	    if(ajStrMatchC(typStr, "ID"))
++		lineType = FLATTYPE_ID;
++	    else if(ajStrMatchC(typStr, "SV") ||
++		    ajStrMatchC(typStr, "IV")) /* emblcds database */
++		lineType = FLATTYPE_VER;
++	    else if(ajStrMatchC(typStr, "AC") ||
++		    ajStrMatchC(typStr, "PA")) /* emblcds database */
++		lineType = FLATTYPE_ACC;
++	    else if(ajStrMatchC(typStr, "DE"))
++		lineType = FLATTYPE_DES;
++	    else if(ajStrMatchC(typStr, "KW"))
++		lineType = FLATTYPE_KEY;
++	    else if(ajStrMatchC(typStr, "OS"))
++		lineType = FLATTYPE_TAX;
++	    else if(ajStrMatchC(typStr, "OC"))
++		lineType = FLATTYPE_TAX;
++	    else
++		lineType=FLATTYPE_OTHER;
++
++	    if(lineType != FLATTYPE_OTHER)
++		ajRegPost(regEmblType, &tmpline);
++	}
++	else
++	    lineType = FLATTYPE_OTHER;
++
++	if(lineType == FLATTYPE_ID)
++	{
++	    ajRegExec(regEmblId, rline);
++	    ajRegSubI(regEmblId, 1, myid);
++	    ajStrFmtUpper(myid);
++	    ajDebug("++id '%S'\n", *myid);
++	    ajRegSubI(regEmblId, 3, &tmpfd);
++	    if(svnfield >= 0 && ajStrGetLen(tmpfd))
++	    {
++		ajStrFmtUpper(&tmpfd);
++		ajStrInsertK(&tmpfd, 0, '.');
++		ajStrInsertS(&tmpfd, 0, *myid);
++		/*ajDebug("++sv '%S'\n", tmpfd);*/
++		embDbiMaxlen(&tmpfd, &maxFieldLen[svnfield]);
++
++		countfield[svnfield]++;
++		if(systemsort)
++		    ajFmtPrintF(alistfile[svnfield], "%S %S\n", *myid, tmpfd);
++		else
++		{
++		    fd = ajCharNewS(tmpfd);
++		    ajListPushAppend(myfdl[svnfield], fd);
++		}
++		svndone = ajTrue;
++	    }
++	    continue;
++	}
++
++	if(lineType == FLATTYPE_ACC && accfield >= 0)
++	{
++	    while(ajRegExec(regEmblAcc, tmpline))
++	    {
++		ajRegSubI(regEmblAcc, 1, &tmpfd);
++		ajStrFmtUpper(&tmpfd);
++		/*ajDebug("++acc '%S'\n", tmpfd);*/
++
++		if(!tmpacnum)
++		    ajStrAssignS(&tmpacnum, tmpfd);
++
++		if((p=strchr(MAJSTRGETPTR(tmpfd),(int)'-')))
++		{
++		    q = p;
++		    while(isdigit((int)*(--q)));
++		    ++q;
++		    ajStrAssignSubC(&tmpstr,q,0,(ajint)(p-q-1));
++		    ajStrToInt(tmpstr,&lo);
++		    fieldwidth = (ajint) (p-q);
++		    ajFmtPrintS(&format,"%%S%%0%dd",fieldwidth);
++
++		    ++p;
++		    q = p;
++		    while(!isdigit((int)*q))
++			++q;
++		    sscanf(q,"%d",&hi);
++		    ajStrAssignSubC(&prefix,p,0,(ajint)(q-p-1));
++	    
++		    if(systemsort)
++		    {
++			for(i=lo;i<=hi;++i)
++			{
++			    ajFmtPrintS(&tmpac,MAJSTRGETPTR(format),prefix,i);
++			    embDbiMaxlen(&tmpac, &maxFieldLen[accfield]);
++			    countfield[accfield]++;
++			    ajFmtPrintF(alistfile[accfield],
++					"%S %S\n", *myid, tmpac);
++			}
++			ajStrDel(&tmpac);
++		    }
++		    else
++		    {
++			for(i=lo;i<=hi;++i)
++			{
++			    ajFmtPrintS(&tmpac,MAJSTRGETPTR(format),prefix,i);
++			    embDbiMaxlen(&tmpac, &maxFieldLen[accfield]);
++			    countfield[accfield]++;
++			    fd = ajCharNewS(tmpac);
++			    ajListPushAppend(myfdl[accfield], fd);
++			}
++			ajStrDel(&tmpac);
++		    }
++		    ajStrDel(&format);
++		    ajStrDel(&prefix);
++		}
++		else {
++		    embDbiMaxlen(&tmpfd, &maxFieldLen[accfield]);
++
++		    countfield[accfield]++;
++		    if(systemsort)
++			ajFmtPrintF(alistfile[accfield],
++				    "%S %S\n", *myid, tmpfd);
++		    else
++		    {
++			fd = ajCharNewS(tmpfd);
++			ajListPushAppend(myfdl[accfield], fd);
++		    }
++		}
++		ajRegPost(regEmblAcc, &tmpstr);
++                ajStrAssignS(&tmpline, tmpstr);
++	    }
++	    continue;
++	}
++	else if(lineType == FLATTYPE_DES && desfield >= 0)
++	{
++            ajStrTrimWhiteStart(&tmpline);
++            for(j=0; swissprefix[j]; j++)
++            {
++                if(ajStrPrefixC(tmpline, swissprefix[j]))
++                    ajStrCutStart(&tmpline, strlen(swissprefix[j]));
++            }
++	    while(ajRegExec(regEmblWrd, tmpline))
++	    {
++		ajRegSubI(regEmblWrd, 1, &tmpfd);
++		ajStrFmtUpper(&tmpfd);
++		/*ajDebug("++des '%S'\n", tmpfd);*/
++		embDbiMaxlen(&tmpfd, &maxFieldLen[desfield]);
++
++		countfield[desfield]++;
++		if(systemsort)
++		    ajFmtPrintF(alistfile[desfield], "%S %S\n", *myid, tmpfd);
++		else
++		{
++		    fd = ajCharNewS(tmpfd);
++		    ajListPushAppend(myfdl[desfield], fd);
++		}
++		ajRegPost(regEmblWrd, &tmpstr);
++                ajStrAssignS(&tmpline, tmpstr);
++	    }
++	    continue;
++	}
++	else if(lineType == FLATTYPE_VER && svnfield >= 0)
++	{
++	    while(ajRegExec(regEmblVer, tmpline))
++	    {
++		ajRegSubI(regEmblVer, 1, &tmpfd);
++		ajStrFmtUpper(&tmpfd);
++		/*ajDebug("++sv '%S'\n", tmpfd);*/
++		embDbiMaxlen(&tmpfd, &maxFieldLen[svnfield]);
++
++		countfield[svnfield]++;
++		if(systemsort)
++		    ajFmtPrintF(alistfile[svnfield], "%S %S\n", *myid, tmpfd);
++		else
++		{
++		    fd = ajCharNewS(tmpfd);
++		    ajListPushAppend(myfdl[svnfield], fd);
++		}
++		ajRegPost(regEmblVer, &tmpstr);	
++                ajStrAssignS(&tmpline, tmpstr);
++            }
++	    svndone = ajTrue;
++	    continue;
++	}
++	else if(lineType == FLATTYPE_KEY && keyfield >= 0)
++	{
++	    while(ajRegExec(regEmblPhr, tmpline))
++	    {
++		ajRegSubI(regEmblPhr, 1, &tmpfd);
++		ajRegPost(regEmblPhr, &tmpstr);
++                ajStrAssignS(&tmpline, tmpstr);
++		ajStrTrimWhiteEnd(&tmpfd);
++		if(!ajStrGetLen(tmpfd))
++		    continue;
++		ajStrFmtUpper(&tmpfd);
++		/*ajDebug("++key '%S'\n", tmpfd);*/
++		embDbiMaxlen(&tmpfd, &maxFieldLen[keyfield]);
++
++		countfield[keyfield]++;
++		if(systemsort)
++		    ajFmtPrintF(alistfile[keyfield], "%S %S\n", *myid, tmpfd);
++		else
++		{
++		    fd = ajCharNewS(tmpfd);
++		    ajListPushAppend(myfdl[keyfield], fd);
++		}
++	    }
++	    continue;
++	}
++	else if(lineType == FLATTYPE_TAX && taxfield >= 0)
++	{
++	    while(ajRegExec(regEmblTax, tmpline))
++	    {
++		ajRegSubI(regEmblTax, 1, &tmpfd);
++		ajRegPost(regEmblTax, &tmpstr);
++                ajStrAssignS(&tmpline, tmpstr);
++		ajStrFmtUpper(&tmpfd);
++		ajStrTrimWhiteEnd(&tmpfd);
++		if(!ajStrGetLen(tmpfd))
++		    continue;
++		/*ajDebug("++tax '%S'\n", tmpfd);*/
++		embDbiMaxlen(&tmpfd, &maxFieldLen[taxfield]);
++
++		countfield[taxfield]++;
++		if(systemsort)
++		    ajFmtPrintF(alistfile[taxfield], "%S %S\n", *myid, tmpfd);
++		else
++		{
++		    fd = ajCharNewS(tmpfd);
++		    ajListPushAppend(myfdl[taxfield], fd);
++		}
++	    }
++	    continue;
++	}
++    }
++
++    if(!done)
++	return ajFalse;
++
++    if(svnfield >= 0 && !svndone && tmpacnum)
++    {
++	ajFmtPrintS(&tmpfd, "%S.0", tmpacnum);
++	embDbiMaxlen(&tmpfd, &maxFieldLen[svnfield]);
++
++	countfield[svnfield]++;
++	if(systemsort)
++	    ajFmtPrintF(alistfile[svnfield], "%S %S\n", *myid, tmpfd);
++	else
++	{
++	    fd = ajCharNewS(tmpfd);
++	    ajListPushAppend(myfdl[svnfield], fd);
++	}
++    }
++
++    ajStrDel(&tmpacnum);
++
++    return ajTrue;
++}
++
++
+ 
+ 
+ /* @funcstatic dbiflat_ParseEmbl **********************************************
+--- emboss-6.4.0.orig/emboss/dbxflat.c
++++ emboss-6.4.0/emboss/dbxflat.c
+@@ -32,6 +32,7 @@
+ static AjBool dbxflat_ParseFastq(EmbPBtreeEntry entry, AjPFile inf);
+ static AjBool dbxflat_ParseEmbl(EmbPBtreeEntry entry, AjPFile inf);
+ static AjBool dbxflat_ParseGenbank(EmbPBtreeEntry entry, AjPFile inf);
++static AjBool dbxflat_ParseSwiss(EmbPBtreeEntry entry, AjPFile inf);
+ 
+ static AjBool dbxflat_NextEntry(EmbPBtreeEntry entry, AjPFile inf);
+ 
+@@ -76,7 +77,7 @@
+ static DbxflatOParser parser[] =
+ {
+     {"EMBL",   dbxflat_ParseEmbl},
+-    {"SWISS",  dbxflat_ParseEmbl},
++    {"SWISS",  dbxflat_ParseSwiss},
+     {"GB",     dbxflat_ParseGenbank},
+     {"REFSEQ", dbxflat_ParseGenbank},
+     {"FASTQ",  dbxflat_ParseFastq},
+@@ -715,6 +716,101 @@
+ 
+ 
+ 
++
++/* @funcstatic dbxflat_ParseSwiss *********************************************
++**
++** Parse the ID, accession from a SwissProt or UniProtKB entry.
++**
++** Reads to the end of the entry and then returns.
++**
++** @param [w] entry [EmbPBtreeEntry] entry
++** @param [u] inf [AjPFile] Input file
++**
++** @return [AjBool] ajTrue on success.
++** @@
++******************************************************************************/
++
++static AjBool dbxflat_ParseSwiss(EmbPBtreeEntry entry, AjPFile inf)
++{
++    AjPStr line = NULL;
++    ajlong pos  = 0L;
++    const char* swissprefix[] = {
++        "RecName: ", "AltName: ", "SubName: ",
++        "Includes:", "Contains:", "Flags: ",
++        "Full=", "Short=", "EC=",
++        "Allergen=", "Biotech=", "CD_antigen=", "INN=",
++        NULL
++    };
++    ajuint i;
++
++    if(!dbxflat_wrdexp)
++	dbxflat_wrdexp = ajRegCompC("([A-Za-z0-9_-]+)");
++
++    line = ajStrNewC("");
++    
++    while(!ajStrPrefixC(line,"//"))
++    {
++	pos = ajFileResetPos(inf);
++	
++	if(!ajReadlineTrim(inf,&line))
++	{
++	    ajStrDel(&line);
++	    return ajFalse;
++	}
++	if(ajStrPrefixC(line,"ID"))
++	{
++	    entry->fpos = pos;
++	    ajFmtScanS(line,"%*S%S",&entry->id);
++	    ajStrTrimEndC(&entry->id, ";");
++/*
++	    ++global;
++	    printf("%d. %s\n",global,ajStrGetPtr(entry->id));
++*/
++	    if(svfield)
++		embBtreeEmblSV(line,svfield->data);
++	}
++
++
++	if(svfield)
++	    if(ajStrPrefixC(line,"SV") ||
++	       ajStrPrefixC(line,"IV"))	/* emblcds database format */
++		embBtreeEmblAC(line,svfield->data);
++
++	if(accfield)
++	    if(ajStrPrefixC(line,"AC") ||
++	       ajStrPrefixC(line,"PA"))	/* emblcds database format */
++		embBtreeEmblAC(line,accfield->data);
++	
++	if(keyfield)
++	    if(ajStrPrefixC(line,"KW"))
++		embBtreeEmblKW(line,keyfield->data,keyfield->len);
++
++	if(desfield)
++	    if(ajStrPrefixC(line,"DE"))
++            {
++                ajStrCutStart(&line, 5);
++                ajStrTrimWhiteStart(&line);
++                for(i=0; swissprefix[i]; i++)
++                {
++                    if(ajStrPrefixC(line, swissprefix[i]))
++                        ajStrCutStart(&line, strlen(swissprefix[i]));
++                }
++		embBtreeParseField(line,dbxflat_wrdexp, desfield);
++            }
++        
++	if(orgfield)
++	    if(ajStrPrefixC(line,"OC") || ajStrPrefixC(line,"OS"))
++		embBtreeEmblTX(line,orgfield->data,orgfield->len);
++    }
++    
++
++    ajStrDel(&line);
++    
++    return ajTrue;
++}
++
++
++
+ 
+ /* @funcstatic dbxflat_NextEntry ********************************************
+ **
+--- emboss-6.4.0.orig/emboss/dbxresource.c
++++ emboss-6.4.0/emboss/dbxresource.c
+@@ -535,6 +535,19 @@
+         if(urlfield && !ajStrMatchC(rest, "None"))
+             embBtreeParseField(rest, dbxresource_wrdexp, urlfield);
+     }
++    else if(ajStrMatchC(name, "NARCat"))
++    {
++        if(catfield && !ajStrMatchC(rest, "None"))
++        {
++            handle = ajStrTokenNewC(rest, "|");
++            while(ajStrTokenNextParse(&handle, &token))
++            {
++                ajStrRemoveWhiteExcess(&token);
++                ajListstrPush(catfield->data,ajStrNewS(token));
++            }
++            ajStrTokenDel(&handle);
++        }
++    }
+     else if(ajStrSuffixC(name, "Cat"))
+     {
+         if(catfield && !ajStrMatchC(rest, "None"))
+--- emboss-6.4.0.orig/emboss/drfinddata.c
++++ emboss-6.4.0/emboss/drfinddata.c
+@@ -155,8 +155,9 @@
+                         {
+                             if(!ajTableMatchS(foundtable, resource->Id))
+                             {
+-                                ajDebug("drcat id '%S' category '%S'\n",
+-                                       resource->Id, resource->Cat);
++                                ajDebug("drcat id '%S' categories %u\n",
++                                        resource->Id,
++                                        ajListGetLength(resource->Cat));
+                                 ajResourceoutWrite(outfile, resource);
+                                 ajTablePut(foundtable, ajStrNewS(resource->Id),
+                                            (void *) 1);
+--- emboss-6.4.0.orig/emboss/drfindformat.c
++++ emboss-6.4.0/emboss/drfindformat.c
+@@ -152,8 +152,9 @@
+                         {
+                             if(!ajTableMatchS(foundtable, resource->Id))
+                             {
+-                                ajDebug("drcat id '%S' category '%S'\n",
+-                                       resource->Id, resource->Cat);
++                                ajDebug("drcat id '%S' categories %u\n",
++                                        resource->Id,
++                                        ajListGetLength(resource->Cat));
+                                 ajResourceoutWrite(outfile, resource);
+                                 ajTablePut(foundtable, ajStrNewS(resource->Id),
+                                            (void *) 1);
+--- emboss-6.4.0.orig/emboss/drfindid.c
++++ emboss-6.4.0/emboss/drfindid.c
+@@ -152,8 +152,9 @@
+                         {
+                             if(!ajTableMatchS(foundtable, resource->Id))
+                             {
+-                                ajDebug("drcat id '%S' category '%S'\n",
+-                                       resource->Id, resource->Cat);
++                                ajDebug("drcat id '%S' categories %u\n",
++                                        resource->Id,
++                                        ajListGetLength(resource->Cat));
+                                 ajResourceoutWrite(outfile, resource);
+                                 ajTablePut(foundtable, ajStrNewS(resource->Id),
+                                            (void *) 1);
+--- emboss-6.4.0.orig/emboss/drfindresource.c
++++ emboss-6.4.0/emboss/drfindresource.c
+@@ -162,9 +162,10 @@
+                         {
+                             if(!ajTableMatchS(foundtable, resource->Id))
+                             {
+-                                ajDebug("drcat id '%S' category '%S'\n",
+-                                       resource->Id, resource->Cat);
+-                                ajResourceoutWrite(outfile, resource);
++                                ajDebug("drcat id '%S' categories %u\n",
++                                        resource->Id,
++                                        ajListGetLength(resource->Cat));
++                                 ajResourceoutWrite(outfile, resource);
+                                 ajTablePut(foundtable, ajStrNewS(resource->Id),
+                                            (void *) 1);
+                             }
+--- emboss-6.4.0.orig/emboss/server.ensemblgenomes
++++ emboss-6.4.0/emboss/server.ensemblgenomes
+@@ -1,4 +1,4 @@
+-# server.ensemblgenomes 2011-07-05 00:00:00
++# server.ensemblgenomes 2011-07-27 00:00:00
+ # Automatically generated by cacheensembl for server 'ensemblgenomes'.
+ 
+ DBNAME acyrthosiphon_pisum [
+@@ -194,6 +194,7 @@
+ ALIAS 15368 brachypodium_distachyon
+ 
+ DBNAME b_afzelii [
++  comment: "SpeciesIdentifier=4"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/borrelia_collection_core_9_62_1a"
+@@ -202,6 +203,7 @@
+ ALIAS 390236 b_afzelii
+ 
+ DBNAME b_amyloliquefaciens [
++  comment: "SpeciesIdentifier=2"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
+@@ -210,6 +212,7 @@
+ ALIAS 326423 b_amyloliquefaciens
+ 
+ DBNAME b_anthracis_a0248 [
++  comment: "SpeciesIdentifier=25"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
+@@ -218,6 +221,7 @@
+ ALIAS 592021 b_anthracis_a0248
+ 
+ DBNAME b_anthracis_ames [
++  comment: "SpeciesIdentifier=3"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
+@@ -226,6 +230,7 @@
+ ALIAS 198094 b_anthracis_ames
+ 
+ DBNAME b_anthracis_ames_ancestor [
++  comment: "SpeciesIdentifier=4"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
+@@ -234,6 +239,7 @@
+ ALIAS 261594 b_anthracis_ames_ancestor
+ 
+ DBNAME b_anthracis_cdc_684 [
++  comment: "SpeciesIdentifier=24"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
+@@ -242,6 +248,7 @@
+ ALIAS 568206 b_anthracis_cdc_684
+ 
+ DBNAME b_anthracis_sterne [
++  comment: "SpeciesIdentifier=5"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
+@@ -250,6 +257,7 @@
+ ALIAS 260799 b_anthracis_sterne
+ 
+ DBNAME b_aphidicola_5a [
++  comment: "SpeciesIdentifier=2"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/buchnera_collection_core_9_62_1a"
+@@ -258,6 +266,7 @@
+ ALIAS 563178 b_aphidicola_5a
+ 
+ DBNAME b_aphidicola_baizongia [
++  comment: "SpeciesIdentifier=5"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/buchnera_collection_core_9_62_1a"
+@@ -266,6 +275,7 @@
+ ALIAS 224915 b_aphidicola_baizongia
+ 
+ DBNAME b_aphidicola_cinara [
++  comment: "SpeciesIdentifier=3"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/buchnera_collection_core_9_62_1a"
+@@ -274,6 +284,7 @@
+ ALIAS 372461 b_aphidicola_cinara
+ 
+ DBNAME b_aphidicola_schizaphis [
++  comment: "SpeciesIdentifier=1"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/buchnera_collection_core_9_62_1a"
+@@ -282,6 +293,7 @@
+ ALIAS 198804 b_aphidicola_schizaphis
+ 
+ DBNAME b_aphidicola_tokyo_1998 [
++  comment: "SpeciesIdentifier=6"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/buchnera_collection_core_9_62_1a"
+@@ -290,6 +302,7 @@
+ ALIAS 107806 b_aphidicola_tokyo_1998
+ 
+ DBNAME b_aphidicola_tuc7 [
++  comment: "SpeciesIdentifier=4"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/buchnera_collection_core_9_62_1a"
+@@ -298,6 +311,7 @@
+ ALIAS 561501 b_aphidicola_tuc7
+ 
+ DBNAME b_burgdorferi_dsm_4680 [
++  comment: "SpeciesIdentifier=8"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/borrelia_collection_core_9_62_1a"
+@@ -306,6 +320,7 @@
+ ALIAS 224326 b_burgdorferi_dsm_4680
+ 
+ DBNAME b_burgdorferi_zs7 [
++  comment: "SpeciesIdentifier=3"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/borrelia_collection_core_9_62_1a"
+@@ -314,6 +329,7 @@
+ ALIAS 445985 b_burgdorferi_zs7
+ 
+ DBNAME b_cereus_03bb102 [
++  comment: "SpeciesIdentifier=20"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
+@@ -322,6 +338,7 @@
+ ALIAS 572264 b_cereus_03bb102
+ 
+ DBNAME b_cereus_172560w [
++  comment: "SpeciesIdentifier=50"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
+@@ -330,6 +347,7 @@
+ ALIAS 526967 b_cereus_172560w
+ 
+ DBNAME b_cereus_95_8201 [
++  comment: "SpeciesIdentifier=36"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
+@@ -338,6 +356,7 @@
+ ALIAS 526979 b_cereus_95_8201
+ 
+ DBNAME b_cereus_ah1271 [
++  comment: "SpeciesIdentifier=71"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
+@@ -346,6 +365,7 @@
+ ALIAS 526992 b_cereus_ah1271
+ 
+ DBNAME b_cereus_ah1272 [
++  comment: "SpeciesIdentifier=53"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
+@@ -354,6 +374,7 @@
+ ALIAS 526993 b_cereus_ah1272
+ 
+ DBNAME b_cereus_ah1273 [
++  comment: "SpeciesIdentifier=43"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
+@@ -362,6 +383,7 @@
+ ALIAS 526994 b_cereus_ah1273
+ 
+ DBNAME b_cereus_ah187 [
++  comment: "SpeciesIdentifier=19"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
+@@ -370,6 +392,7 @@
+ ALIAS 405534 b_cereus_ah187
+ 
+ DBNAME b_cereus_ah603 [
++  comment: "SpeciesIdentifier=49"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
+@@ -378,6 +401,7 @@
+ ALIAS 526990 b_cereus_ah603
+ 
+ DBNAME b_cereus_ah621 [
++  comment: "SpeciesIdentifier=46"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
+@@ -386,6 +410,7 @@
+ ALIAS 526972 b_cereus_ah621
+ 
+ DBNAME b_cereus_ah676 [
++  comment: "SpeciesIdentifier=38"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
+@@ -394,6 +419,7 @@
+ ALIAS 526991 b_cereus_ah676
+ 
+ DBNAME b_cereus_ah820 [
++  comment: "SpeciesIdentifier=18"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
+@@ -402,6 +428,7 @@
+ ALIAS 405535 b_cereus_ah820
+ 
+ DBNAME b_cereus_atcc_10876 [
++  comment: "SpeciesIdentifier=70"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
+@@ -410,6 +437,7 @@
+ ALIAS 526980 b_cereus_atcc_10876
+ 
+ DBNAME b_cereus_atcc_10987 [
++  comment: "SpeciesIdentifier=6"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
+@@ -418,6 +446,7 @@
+ ALIAS 222523 b_cereus_atcc_10987
+ 
+ DBNAME b_cereus_atcc_14579 [
++  comment: "SpeciesIdentifier=7"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
+@@ -426,6 +455,7 @@
+ ALIAS 226900 b_cereus_atcc_14579
+ 
+ DBNAME b_cereus_atcc_4342 [
++  comment: "SpeciesIdentifier=72"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
+@@ -434,6 +464,7 @@
+ ALIAS 526977 b_cereus_atcc_4342
+ 
+ DBNAME b_cereus_b4264 [
++  comment: "SpeciesIdentifier=23"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
+@@ -442,6 +473,7 @@
+ ALIAS 405532 b_cereus_b4264
+ 
+ DBNAME b_cereus_bdrd_bcer4 [
++  comment: "SpeciesIdentifier=62"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
+@@ -450,6 +482,7 @@
+ ALIAS 526978 b_cereus_bdrd_bcer4
+ 
+ DBNAME b_cereus_bdrd_st196 [
++  comment: "SpeciesIdentifier=34"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
+@@ -458,6 +491,7 @@
+ ALIAS 526976 b_cereus_bdrd_st196
+ 
+ DBNAME b_cereus_bdrd_st24 [
++  comment: "SpeciesIdentifier=37"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
+@@ -466,6 +500,7 @@
+ ALIAS 526974 b_cereus_bdrd_st24
+ 
+ DBNAME b_cereus_bdrd_st26 [
++  comment: "SpeciesIdentifier=39"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
+@@ -474,6 +509,7 @@
+ ALIAS 526975 b_cereus_bdrd_st26
+ 
+ DBNAME b_cereus_bgsc_6e1 [
++  comment: "SpeciesIdentifier=67"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
+@@ -482,6 +518,7 @@
+ ALIAS 526970 b_cereus_bgsc_6e1
+ 
+ DBNAME b_cereus_cytotoxis [
++  comment: "SpeciesIdentifier=8"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
+@@ -490,6 +527,7 @@
+ ALIAS 315749 b_cereus_cytotoxis
+ 
+ DBNAME b_cereus_f65185 [
++  comment: "SpeciesIdentifier=30"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
+@@ -498,6 +536,7 @@
+ ALIAS 526989 b_cereus_f65185
+ 
+ DBNAME b_cereus_g9842 [
++  comment: "SpeciesIdentifier=22"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
+@@ -506,6 +545,7 @@
+ ALIAS 405531 b_cereus_g9842
+ 
+ DBNAME b_cereus_m1293 [
++  comment: "SpeciesIdentifier=40"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
+@@ -514,6 +554,7 @@
+ ALIAS 526973 b_cereus_m1293
+ 
+ DBNAME b_cereus_mm1550 [
++  comment: "SpeciesIdentifier=65"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
+@@ -522,6 +563,7 @@
+ ALIAS 526969 b_cereus_mm1550
+ 
+ DBNAME b_cereus_mm3 [
++  comment: "SpeciesIdentifier=52"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
+@@ -530,6 +572,7 @@
+ ALIAS 526971 b_cereus_mm3
+ 
+ DBNAME b_cereus_q1 [
++  comment: "SpeciesIdentifier=21"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
+@@ -538,6 +581,7 @@
+ ALIAS 361100 b_cereus_q1
+ 
+ DBNAME b_cereus_r309803 [
++  comment: "SpeciesIdentifier=33"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
+@@ -546,6 +590,7 @@
+ ALIAS 526968 b_cereus_r309803
+ 
+ DBNAME b_cereus_rock1_15 [
++  comment: "SpeciesIdentifier=42"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
+@@ -554,6 +599,7 @@
+ ALIAS 526982 b_cereus_rock1_15
+ 
+ DBNAME b_cereus_rock1_3 [
++  comment: "SpeciesIdentifier=78"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
+@@ -562,6 +608,7 @@
+ ALIAS 526981 b_cereus_rock1_3
+ 
+ DBNAME b_cereus_rock3_28 [
++  comment: "SpeciesIdentifier=57"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
+@@ -570,6 +617,7 @@
+ ALIAS 526983 b_cereus_rock3_28
+ 
+ DBNAME b_cereus_rock3_29 [
++  comment: "SpeciesIdentifier=51"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
+@@ -578,6 +626,7 @@
+ ALIAS 526984 b_cereus_rock3_29
+ 
+ DBNAME b_cereus_rock3_42 [
++  comment: "SpeciesIdentifier=77"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
+@@ -586,6 +635,7 @@
+ ALIAS 526985 b_cereus_rock3_42
+ 
+ DBNAME b_cereus_rock3_44 [
++  comment: "SpeciesIdentifier=48"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
+@@ -594,6 +644,7 @@
+ ALIAS 526986 b_cereus_rock3_44
+ 
+ DBNAME b_cereus_rock4_18 [
++  comment: "SpeciesIdentifier=55"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
+@@ -602,6 +653,7 @@
+ ALIAS 526988 b_cereus_rock4_18
+ 
+ DBNAME b_cereus_rock4_2 [
++  comment: "SpeciesIdentifier=76"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
+@@ -610,6 +662,7 @@
+ ALIAS 526987 b_cereus_rock4_2
+ 
+ DBNAME b_cereus_var_anthracis [
++  comment: "SpeciesIdentifier=69"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
+@@ -618,6 +671,7 @@
+ ALIAS 637380 b_cereus_var_anthracis
+ 
+ DBNAME b_cereus_zk [
++  comment: "SpeciesIdentifier=9"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
+@@ -626,6 +680,7 @@
+ ALIAS 288681 b_cereus_zk
+ 
+ DBNAME b_clausii [
++  comment: "SpeciesIdentifier=10"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
+@@ -634,6 +689,7 @@
+ ALIAS 66692 b_clausii
+ 
+ DBNAME b_duttonii [
++  comment: "SpeciesIdentifier=2"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/borrelia_collection_core_9_62_1a"
+@@ -642,6 +698,7 @@
+ ALIAS 412419 b_duttonii
+ 
+ DBNAME b_garinii [
++  comment: "SpeciesIdentifier=7"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/borrelia_collection_core_9_62_1a"
+@@ -650,6 +707,7 @@
+ ALIAS 290434 b_garinii
+ 
+ DBNAME b_halodurans [
++  comment: "SpeciesIdentifier=11"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
+@@ -658,6 +716,7 @@
+ ALIAS 272558 b_halodurans
+ 
+ DBNAME b_hermsii [
++  comment: "SpeciesIdentifier=6"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/borrelia_collection_core_9_62_1a"
+@@ -666,6 +725,7 @@
+ ALIAS 314723 b_hermsii
+ 
+ DBNAME b_licheniformis_goettingen [
++  comment: "SpeciesIdentifier=12"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
+@@ -674,6 +734,7 @@
+ ALIAS 279010 b_licheniformis_goettingen
+ 
+ DBNAME b_licheniformis_novozymes [
++  comment: "SpeciesIdentifier=13"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
+@@ -681,6 +742,7 @@
+ 
+ 
+ DBNAME b_megaterium_atcc_12872 [
++  comment: "SpeciesIdentifier=73"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
+@@ -689,6 +751,7 @@
+ ALIAS 545693 b_megaterium_atcc_12872
+ 
+ DBNAME b_megaterium_dsm_319 [
++  comment: "SpeciesIdentifier=80"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
+@@ -697,6 +760,7 @@
+ ALIAS 592022 b_megaterium_dsm_319
+ 
+ DBNAME b_mycoides_dsm_2048 [
++  comment: "SpeciesIdentifier=47"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
+@@ -705,6 +769,7 @@
+ ALIAS 526997 b_mycoides_dsm_2048
+ 
+ DBNAME b_mycoides_rock1_4 [
++  comment: "SpeciesIdentifier=28"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
+@@ -713,6 +778,7 @@
+ ALIAS 526998 b_mycoides_rock1_4
+ 
+ DBNAME b_mycoides_rock3_17 [
++  comment: "SpeciesIdentifier=59"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
+@@ -721,6 +787,7 @@
+ ALIAS 526999 b_mycoides_rock3_17
+ 
+ DBNAME b_pseudofirmus [
++  comment: "SpeciesIdentifier=54"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
+@@ -729,6 +796,7 @@
+ ALIAS 398511 b_pseudofirmus
+ 
+ DBNAME b_pseudomycoides [
++  comment: "SpeciesIdentifier=58"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
+@@ -737,6 +805,7 @@
+ ALIAS 527000 b_pseudomycoides
+ 
+ DBNAME b_pumilus [
++  comment: "SpeciesIdentifier=14"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
+@@ -745,6 +814,7 @@
+ ALIAS 315750 b_pumilus
+ 
+ DBNAME b_recurrentis [
++  comment: "SpeciesIdentifier=5"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/borrelia_collection_core_9_62_1a"
+@@ -753,6 +823,7 @@
+ ALIAS 412418 b_recurrentis
+ 
+ DBNAME b_selenitireducens [
++  comment: "SpeciesIdentifier=32"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
+@@ -761,6 +832,7 @@
+ ALIAS 439292 b_selenitireducens
+ 
+ DBNAME b_subtilis [
++  comment: "SpeciesIdentifier=1"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
+@@ -769,6 +841,7 @@
+ ALIAS 224308 b_subtilis
+ 
+ DBNAME b_thuringiensis [
++  comment: "SpeciesIdentifier=15"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
+@@ -777,6 +850,7 @@
+ ALIAS 412694 b_thuringiensis
+ 
+ DBNAME b_thuringiensis_atcc_10792 [
++  comment: "SpeciesIdentifier=41"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
+@@ -785,6 +859,7 @@
+ ALIAS 527031 b_thuringiensis_atcc_10792
+ 
+ DBNAME b_thuringiensis_bgsc_4aj1 [
++  comment: "SpeciesIdentifier=75"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
+@@ -793,6 +868,7 @@
+ ALIAS 527022 b_thuringiensis_bgsc_4aj1
+ 
+ DBNAME b_thuringiensis_bgsc_4aw1_andalous [
++  comment: "SpeciesIdentifier=56"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
+@@ -801,6 +877,7 @@
+ ALIAS 527032 b_thuringiensis_bgsc_4aw1_andalous
+ 
+ DBNAME b_thuringiensis_bgsc_4ba1_pondicheri [
++  comment: "SpeciesIdentifier=29"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
+@@ -809,6 +886,7 @@
+ ALIAS 527029 b_thuringiensis_bgsc_4ba1_pondicheri
+ 
+ DBNAME b_thuringiensis_bgsc_4bd1_huazhong [
++  comment: "SpeciesIdentifier=31"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
+@@ -817,6 +895,7 @@
+ ALIAS 527030 b_thuringiensis_bgsc_4bd1_huazhong
+ 
+ DBNAME b_thuringiensis_bgsc_4cc1_pulsiensis [
++  comment: "SpeciesIdentifier=35"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
+@@ -825,6 +904,7 @@
+ ALIAS 527028 b_thuringiensis_bgsc_4cc1_pulsiensis
+ 
+ DBNAME b_thuringiensis_bgsc_4y1_tochigiensis [
++  comment: "SpeciesIdentifier=44"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
+@@ -833,6 +913,7 @@
+ ALIAS 527024 b_thuringiensis_bgsc_4y1_tochigiensis
+ 
+ DBNAME b_thuringiensis_bmb171 [
++  comment: "SpeciesIdentifier=68"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
+@@ -841,6 +922,7 @@
+ ALIAS 714359 b_thuringiensis_bmb171
+ 
+ DBNAME b_thuringiensis_bt407 [
++  comment: "SpeciesIdentifier=26"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
+@@ -849,6 +931,7 @@
+ ALIAS 527021 b_thuringiensis_bt407
+ 
+ DBNAME b_thuringiensis_ibl200 [
++  comment: "SpeciesIdentifier=27"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
+@@ -857,6 +940,7 @@
+ ALIAS 527019 b_thuringiensis_ibl200
+ 
+ DBNAME b_thuringiensis_ibl4222 [
++  comment: "SpeciesIdentifier=64"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
+@@ -865,6 +949,7 @@
+ ALIAS 527020 b_thuringiensis_ibl4222
+ 
+ DBNAME b_thuringiensis_konkukian [
++  comment: "SpeciesIdentifier=16"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
+@@ -873,6 +958,7 @@
+ ALIAS 281309 b_thuringiensis_konkukian
+ 
+ DBNAME b_thuringiensis_t01001 [
++  comment: "SpeciesIdentifier=60"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
+@@ -881,6 +967,7 @@
+ ALIAS 527025 b_thuringiensis_t01001
+ 
+ DBNAME b_thuringiensis_t03a001_kurstaki [
++  comment: "SpeciesIdentifier=63"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
+@@ -889,6 +976,7 @@
+ ALIAS 527023 b_thuringiensis_t03a001_kurstaki
+ 
+ DBNAME b_thuringiensis_t04001_sotto [
++  comment: "SpeciesIdentifier=61"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
+@@ -897,6 +985,7 @@
+ ALIAS 527026 b_thuringiensis_t04001_sotto
+ 
+ DBNAME b_thuringiensis_t13001_pakistani [
++  comment: "SpeciesIdentifier=45"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
+@@ -905,6 +994,7 @@
+ ALIAS 527027 b_thuringiensis_t13001_pakistani
+ 
+ DBNAME b_turicatae [
++  comment: "SpeciesIdentifier=1"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/borrelia_collection_core_9_62_1a"
+@@ -913,6 +1003,7 @@
+ ALIAS 314724 b_turicatae
+ 
+ DBNAME b_tusciae [
++  comment: "SpeciesIdentifier=79"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
+@@ -921,6 +1012,7 @@
+ ALIAS 562970 b_tusciae
+ 
+ DBNAME b_weihenstephanensis [
++  comment: "SpeciesIdentifier=17"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/bacillus_collection_core_9_62_4a"
+@@ -1221,6 +1313,7 @@
+ ]
+ 
+ DBNAME e_coli_042 [
++  comment: "SpeciesIdentifier=43"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_core_9_62_5a"
+@@ -1229,12 +1322,14 @@
+ ALIAS 216592 e_coli_042
+ 
+ DBNAME e_coli_042_funcgen [
++  comment: "SpeciesIdentifier=43"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_funcgen_9_62_5a"
+ ]
+ 
+ DBNAME e_coli_55989 [
++  comment: "SpeciesIdentifier=26"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_core_9_62_5a"
+@@ -1243,12 +1338,14 @@
+ ALIAS 585055 e_coli_55989
+ 
+ DBNAME e_coli_55989_funcgen [
++  comment: "SpeciesIdentifier=26"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_funcgen_9_62_5a"
+ ]
+ 
+ DBNAME e_coli_atcc_27325 [
++  comment: "SpeciesIdentifier=4"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_core_9_62_5a"
+@@ -1257,12 +1354,14 @@
+ ALIAS 316407 e_coli_atcc_27325
+ 
+ DBNAME e_coli_atcc_27325_funcgen [
++  comment: "SpeciesIdentifier=4"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_funcgen_9_62_5a"
+ ]
+ 
+ DBNAME e_coli_atcc_33849 [
++  comment: "SpeciesIdentifier=39"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_core_9_62_5a"
+@@ -1271,12 +1370,14 @@
+ ALIAS 536056 e_coli_atcc_33849
+ 
+ DBNAME e_coli_atcc_33849_funcgen [
++  comment: "SpeciesIdentifier=39"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_funcgen_9_62_5a"
+ ]
+ 
+ DBNAME e_coli_atcc_8739 [
++  comment: "SpeciesIdentifier=2"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_core_9_62_5a"
+@@ -1285,12 +1386,14 @@
+ ALIAS 481805 e_coli_atcc_8739
+ 
+ DBNAME e_coli_atcc_8739_funcgen [
++  comment: "SpeciesIdentifier=2"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_funcgen_9_62_5a"
+ ]
+ 
+ DBNAME e_coli_bl21 [
++  comment: "SpeciesIdentifier=32"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_core_9_62_5a"
+@@ -1299,12 +1402,14 @@
+ ALIAS 511693 e_coli_bl21
+ 
+ DBNAME e_coli_bl21_funcgen [
++  comment: "SpeciesIdentifier=32"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_funcgen_9_62_5a"
+ ]
+ 
+ DBNAME e_coli_bl21_de3_jgi [
++  comment: "SpeciesIdentifier=40"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_core_9_62_5a"
+@@ -1313,12 +1418,14 @@
+ ALIAS 866768 e_coli_bl21_de3_jgi
+ 
+ DBNAME e_coli_bl21_de3_jgi_funcgen [
++  comment: "SpeciesIdentifier=40"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_funcgen_9_62_5a"
+ ]
+ 
+ DBNAME e_coli_bl21_de3_kribb [
++  comment: "SpeciesIdentifier=38"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_core_9_62_5a"
+@@ -1327,12 +1434,14 @@
+ ALIAS 469008 e_coli_bl21_de3_kribb
+ 
+ DBNAME e_coli_bl21_de3_kribb_funcgen [
++  comment: "SpeciesIdentifier=38"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_funcgen_9_62_5a"
+ ]
+ 
+ DBNAME e_coli_bw2952 [
++  comment: "SpeciesIdentifier=31"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_core_9_62_5a"
+@@ -1341,12 +1450,14 @@
+ ALIAS 595496 e_coli_bw2952
+ 
+ DBNAME e_coli_bw2952_funcgen [
++  comment: "SpeciesIdentifier=31"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_funcgen_9_62_5a"
+ ]
+ 
+ DBNAME e_coli_dh10b [
++  comment: "SpeciesIdentifier=3"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_core_9_62_5a"
+@@ -1355,12 +1466,14 @@
+ ALIAS 316385 e_coli_dh10b
+ 
+ DBNAME e_coli_dh10b_funcgen [
++  comment: "SpeciesIdentifier=3"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_funcgen_9_62_5a"
+ ]
+ 
+ DBNAME e_coli_ec4115 [
++  comment: "SpeciesIdentifier=7"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_core_9_62_5a"
+@@ -1369,12 +1482,14 @@
+ ALIAS 444450 e_coli_ec4115
+ 
+ DBNAME e_coli_ec4115_funcgen [
++  comment: "SpeciesIdentifier=7"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_funcgen_9_62_5a"
+ ]
+ 
+ DBNAME e_coli_edl933 [
++  comment: "SpeciesIdentifier=6"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_core_9_62_5a"
+@@ -1383,12 +1498,14 @@
+ ALIAS 155864 e_coli_edl933
+ 
+ DBNAME e_coli_edl933_funcgen [
++  comment: "SpeciesIdentifier=6"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_funcgen_9_62_5a"
+ ]
+ 
+ DBNAME e_coli_k12 [
++  comment: "SpeciesIdentifier=1"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_core_9_62_5a"
+@@ -1397,12 +1514,14 @@
+ ALIAS 511145 e_coli_k12
+ 
+ DBNAME e_coli_k12_funcgen [
++  comment: "SpeciesIdentifier=1"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_funcgen_9_62_5a"
+ ]
+ 
+ DBNAME e_coli_o103_h2 [
++  comment: "SpeciesIdentifier=36"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_core_9_62_5a"
+@@ -1411,12 +1530,14 @@
+ ALIAS 585395 e_coli_o103_h2
+ 
+ DBNAME e_coli_o103_h2_funcgen [
++  comment: "SpeciesIdentifier=36"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_funcgen_9_62_5a"
+ ]
+ 
+ DBNAME e_coli_o111_h_ [
++  comment: "SpeciesIdentifier=37"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_core_9_62_5a"
+@@ -1425,12 +1546,14 @@
+ ALIAS 585396 e_coli_o111_h_
+ 
+ DBNAME e_coli_o111_h__funcgen [
++  comment: "SpeciesIdentifier=37"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_funcgen_9_62_5a"
+ ]
+ 
+ DBNAME e_coli_o127_h6 [
++  comment: "SpeciesIdentifier=23"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_core_9_62_5a"
+@@ -1439,12 +1562,14 @@
+ ALIAS 574521 e_coli_o127_h6
+ 
+ DBNAME e_coli_o127_h6_funcgen [
++  comment: "SpeciesIdentifier=23"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_funcgen_9_62_5a"
+ ]
+ 
+ DBNAME e_coli_o139_h28 [
++  comment: "SpeciesIdentifier=5"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_core_9_62_5a"
+@@ -1453,12 +1578,14 @@
+ ALIAS 331111 e_coli_o139_h28
+ 
+ DBNAME e_coli_o139_h28_funcgen [
++  comment: "SpeciesIdentifier=5"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_funcgen_9_62_5a"
+ ]
+ 
+ DBNAME e_coli_o157_h7_tw14588 [
++  comment: "SpeciesIdentifier=45"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_core_9_62_5a"
+@@ -1467,12 +1594,14 @@
+ ALIAS 502346 e_coli_o157_h7_tw14588
+ 
+ DBNAME e_coli_o157_h7_tw14588_funcgen [
++  comment: "SpeciesIdentifier=45"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_funcgen_9_62_5a"
+ ]
+ 
+ DBNAME e_coli_o17_k52_h18 [
++  comment: "SpeciesIdentifier=24"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_core_9_62_5a"
+@@ -1481,12 +1610,14 @@
+ ALIAS 585056 e_coli_o17_k52_h18
+ 
+ DBNAME e_coli_o17_k52_h18_funcgen [
++  comment: "SpeciesIdentifier=24"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_funcgen_9_62_5a"
+ ]
+ 
+ DBNAME e_coli_o18_k1_h7 [
++  comment: "SpeciesIdentifier=46"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_core_9_62_5a"
+@@ -1495,12 +1626,14 @@
+ ALIAS 714962 e_coli_o18_k1_h7
+ 
+ DBNAME e_coli_o18_k1_h7_funcgen [
++  comment: "SpeciesIdentifier=46"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_funcgen_9_62_5a"
+ ]
+ 
+ DBNAME e_coli_o1_k1_apec [
++  comment: "SpeciesIdentifier=8"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_core_9_62_5a"
+@@ -1509,12 +1642,14 @@
+ ALIAS 405955 e_coli_o1_k1_apec
+ 
+ DBNAME e_coli_o1_k1_apec_funcgen [
++  comment: "SpeciesIdentifier=8"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_funcgen_9_62_5a"
+ ]
+ 
+ DBNAME e_coli_o26_h11 [
++  comment: "SpeciesIdentifier=35"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_core_9_62_5a"
+@@ -1523,12 +1658,14 @@
+ ALIAS 573235 e_coli_o26_h11
+ 
+ DBNAME e_coli_o26_h11_funcgen [
++  comment: "SpeciesIdentifier=35"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_funcgen_9_62_5a"
+ ]
+ 
+ DBNAME e_coli_o45_k1 [
++  comment: "SpeciesIdentifier=28"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_core_9_62_5a"
+@@ -1537,12 +1674,14 @@
+ ALIAS 585035 e_coli_o45_k1
+ 
+ DBNAME e_coli_o45_k1_funcgen [
++  comment: "SpeciesIdentifier=28"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_funcgen_9_62_5a"
+ ]
+ 
+ DBNAME e_coli_o55_h7 [
++  comment: "SpeciesIdentifier=44"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_core_9_62_5a"
+@@ -1551,12 +1690,14 @@
+ ALIAS 701177 e_coli_o55_h7
+ 
+ DBNAME e_coli_o55_h7_funcgen [
++  comment: "SpeciesIdentifier=44"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_funcgen_9_62_5a"
+ ]
+ 
+ DBNAME e_coli_o6 [
++  comment: "SpeciesIdentifier=9"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_core_9_62_5a"
+@@ -1565,12 +1706,14 @@
+ ALIAS 217992 e_coli_o6
+ 
+ DBNAME e_coli_o6_funcgen [
++  comment: "SpeciesIdentifier=9"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_funcgen_9_62_5a"
+ ]
+ 
+ DBNAME e_coli_o6_k15_h31 [
++  comment: "SpeciesIdentifier=10"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_core_9_62_5a"
+@@ -1579,12 +1722,14 @@
+ ALIAS 362663 e_coli_o6_k15_h31
+ 
+ DBNAME e_coli_o6_k15_h31_funcgen [
++  comment: "SpeciesIdentifier=10"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_funcgen_9_62_5a"
+ ]
+ 
+ DBNAME e_coli_o7_k1 [
++  comment: "SpeciesIdentifier=30"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_core_9_62_5a"
+@@ -1593,12 +1738,14 @@
+ ALIAS 585057 e_coli_o7_k1
+ 
+ DBNAME e_coli_o7_k1_funcgen [
++  comment: "SpeciesIdentifier=30"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_funcgen_9_62_5a"
+ ]
+ 
+ DBNAME e_coli_o8 [
++  comment: "SpeciesIdentifier=27"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_core_9_62_5a"
+@@ -1607,12 +1754,14 @@
+ ALIAS 585034 e_coli_o8
+ 
+ DBNAME e_coli_o8_funcgen [
++  comment: "SpeciesIdentifier=27"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_funcgen_9_62_5a"
+ ]
+ 
+ DBNAME e_coli_o81 [
++  comment: "SpeciesIdentifier=29"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_core_9_62_5a"
+@@ -1621,12 +1770,14 @@
+ ALIAS 585397 e_coli_o81
+ 
+ DBNAME e_coli_o81_funcgen [
++  comment: "SpeciesIdentifier=29"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_funcgen_9_62_5a"
+ ]
+ 
+ DBNAME e_coli_o9_h4 [
++  comment: "SpeciesIdentifier=11"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_core_9_62_5a"
+@@ -1635,12 +1786,14 @@
+ ALIAS 331112 e_coli_o9_h4
+ 
+ DBNAME e_coli_o9_h4_funcgen [
++  comment: "SpeciesIdentifier=11"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_funcgen_9_62_5a"
+ ]
+ 
+ DBNAME e_coli_rel606 [
++  comment: "SpeciesIdentifier=33"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_core_9_62_5a"
+@@ -1649,12 +1802,14 @@
+ ALIAS 413997 e_coli_rel606
+ 
+ DBNAME e_coli_rel606_funcgen [
++  comment: "SpeciesIdentifier=33"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_funcgen_9_62_5a"
+ ]
+ 
+ DBNAME e_coli_sakai [
++  comment: "SpeciesIdentifier=12"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_core_9_62_5a"
+@@ -1663,12 +1818,14 @@
+ ALIAS 386585 e_coli_sakai
+ 
+ DBNAME e_coli_sakai_funcgen [
++  comment: "SpeciesIdentifier=12"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_funcgen_9_62_5a"
+ ]
+ 
+ DBNAME e_coli_se11 [
++  comment: "SpeciesIdentifier=22"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_core_9_62_5a"
+@@ -1677,12 +1834,14 @@
+ ALIAS 409438 e_coli_se11
+ 
+ DBNAME e_coli_se11_funcgen [
++  comment: "SpeciesIdentifier=22"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_funcgen_9_62_5a"
+ ]
+ 
+ DBNAME e_coli_se15 [
++  comment: "SpeciesIdentifier=42"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_core_9_62_5a"
+@@ -1691,12 +1850,14 @@
+ ALIAS 431946 e_coli_se15
+ 
+ DBNAME e_coli_se15_funcgen [
++  comment: "SpeciesIdentifier=42"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_funcgen_9_62_5a"
+ ]
+ 
+ DBNAME e_coli_sms_3_5 [
++  comment: "SpeciesIdentifier=13"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_core_9_62_5a"
+@@ -1705,12 +1866,14 @@
+ ALIAS 439855 e_coli_sms_3_5
+ 
+ DBNAME e_coli_sms_3_5_funcgen [
++  comment: "SpeciesIdentifier=13"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_funcgen_9_62_5a"
+ ]
+ 
+ DBNAME e_coli_tw14359 [
++  comment: "SpeciesIdentifier=34"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_core_9_62_5a"
+@@ -1719,12 +1882,14 @@
+ ALIAS 544404 e_coli_tw14359
+ 
+ DBNAME e_coli_tw14359_funcgen [
++  comment: "SpeciesIdentifier=34"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_funcgen_9_62_5a"
+ ]
+ 
+ DBNAME e_coli_uti89 [
++  comment: "SpeciesIdentifier=14"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_core_9_62_5a"
+@@ -1733,12 +1898,14 @@
+ ALIAS 364106 e_coli_uti89
+ 
+ DBNAME e_coli_uti89_funcgen [
++  comment: "SpeciesIdentifier=14"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_funcgen_9_62_5a"
+ ]
+ 
+ DBNAME e_fergusonii [
++  comment: "SpeciesIdentifier=25"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_core_9_62_5a"
+@@ -1747,6 +1914,7 @@
+ ALIAS 585054 e_fergusonii
+ 
+ DBNAME e_fergusonii_funcgen [
++  comment: "SpeciesIdentifier=25"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_funcgen_9_62_5a"
+@@ -1843,6 +2011,7 @@
+ ]
+ 
+ DBNAME mycobacterium_sp_jls [
++  comment: "SpeciesIdentifier=11"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/mycobacterium_collection_core_9_62_3a"
+@@ -1851,6 +2020,7 @@
+ ALIAS 164757 mycobacterium_sp_jls
+ 
+ DBNAME mycobacterium_sp_kms [
++  comment: "SpeciesIdentifier=12"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/mycobacterium_collection_core_9_62_3a"
+@@ -1859,6 +2029,7 @@
+ ALIAS 189918 mycobacterium_sp_kms
+ 
+ DBNAME mycobacterium_sp_mcs [
++  comment: "SpeciesIdentifier=13"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/mycobacterium_collection_core_9_62_3a"
+@@ -1867,6 +2038,7 @@
+ ALIAS 164756 mycobacterium_sp_mcs
+ 
+ DBNAME m_abscessus [
++  comment: "SpeciesIdentifier=2"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/mycobacterium_collection_core_9_62_3a"
+@@ -1875,6 +2047,7 @@
+ ALIAS 36809 m_abscessus
+ 
+ DBNAME m_avium [
++  comment: "SpeciesIdentifier=3"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/mycobacterium_collection_core_9_62_3a"
+@@ -1883,6 +2056,7 @@
+ ALIAS 243243 m_avium
+ 
+ DBNAME m_bovis_af2122_97 [
++  comment: "SpeciesIdentifier=4"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/mycobacterium_collection_core_9_62_3a"
+@@ -1891,6 +2065,7 @@
+ ALIAS 233413 m_bovis_af2122_97
+ 
+ DBNAME m_bovis_pasteur_1173p2 [
++  comment: "SpeciesIdentifier=5"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/mycobacterium_collection_core_9_62_3a"
+@@ -1899,6 +2074,7 @@
+ ALIAS 410289 m_bovis_pasteur_1173p2
+ 
+ DBNAME m_bovis_tokyo_172 [
++  comment: "SpeciesIdentifier=19"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/mycobacterium_collection_core_9_62_3a"
+@@ -1907,6 +2083,7 @@
+ ALIAS 561275 m_bovis_tokyo_172
+ 
+ DBNAME m_gilvum [
++  comment: "SpeciesIdentifier=6"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/mycobacterium_collection_core_9_62_3a"
+@@ -1915,6 +2092,7 @@
+ ALIAS 350054 m_gilvum
+ 
+ DBNAME m_leprae_br4923 [
++  comment: "SpeciesIdentifier=18"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/mycobacterium_collection_core_9_62_3a"
+@@ -1923,6 +2101,7 @@
+ ALIAS 561304 m_leprae_br4923
+ 
+ DBNAME m_leprae_tn [
++  comment: "SpeciesIdentifier=7"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/mycobacterium_collection_core_9_62_3a"
+@@ -1931,6 +2110,7 @@
+ ALIAS 272631 m_leprae_tn
+ 
+ DBNAME m_marinum [
++  comment: "SpeciesIdentifier=8"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/mycobacterium_collection_core_9_62_3a"
+@@ -1939,6 +2119,7 @@
+ ALIAS 216594 m_marinum
+ 
+ DBNAME m_paratuberculosis [
++  comment: "SpeciesIdentifier=9"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/mycobacterium_collection_core_9_62_3a"
+@@ -1947,6 +2128,7 @@
+ ALIAS 262316 m_paratuberculosis
+ 
+ DBNAME m_smegmatis [
++  comment: "SpeciesIdentifier=10"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/mycobacterium_collection_core_9_62_3a"
+@@ -1955,6 +2137,7 @@
+ ALIAS 246196 m_smegmatis
+ 
+ DBNAME m_tuberculosis_atcc_25177 [
++  comment: "SpeciesIdentifier=14"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/mycobacterium_collection_core_9_62_3a"
+@@ -1963,6 +2146,7 @@
+ ALIAS 419947 m_tuberculosis_atcc_25177
+ 
+ DBNAME m_tuberculosis_cdc1551 [
++  comment: "SpeciesIdentifier=15"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/mycobacterium_collection_core_9_62_3a"
+@@ -1971,6 +2155,7 @@
+ ALIAS 83331 m_tuberculosis_cdc1551
+ 
+ DBNAME m_tuberculosis_h37rv [
++  comment: "SpeciesIdentifier=1"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/mycobacterium_collection_core_9_62_3a"
+@@ -1979,6 +2164,7 @@
+ ALIAS 83332 m_tuberculosis_h37rv
+ 
+ DBNAME m_tuberculosis_kzn_1435 [
++  comment: "SpeciesIdentifier=21"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/mycobacterium_collection_core_9_62_3a"
+@@ -1987,6 +2173,7 @@
+ ALIAS 478434 m_tuberculosis_kzn_1435
+ 
+ DBNAME m_ulcerans [
++  comment: "SpeciesIdentifier=16"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/mycobacterium_collection_core_9_62_3a"
+@@ -1995,6 +2182,7 @@
+ ALIAS 362242 m_ulcerans
+ 
+ DBNAME m_vanbaalenii [
++  comment: "SpeciesIdentifier=17"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/mycobacterium_collection_core_9_62_3a"
+@@ -2030,6 +2218,7 @@
+ ALIAS n_crassa neurospora_crassa
+ 
+ DBNAME n_gonorrhoeae_atcc_700825 [
++  comment: "SpeciesIdentifier=2"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/neisseria_collection_core_9_62_3a"
+@@ -2038,6 +2227,7 @@
+ ALIAS 242231 n_gonorrhoeae_atcc_700825
+ 
+ DBNAME n_gonorrhoeae_nccp11945 [
++  comment: "SpeciesIdentifier=3"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/neisseria_collection_core_9_62_3a"
+@@ -2046,6 +2236,7 @@
+ ALIAS 521006 n_gonorrhoeae_nccp11945
+ 
+ DBNAME n_meningitidis_053442 [
++  comment: "SpeciesIdentifier=6"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/neisseria_collection_core_9_62_3a"
+@@ -2054,6 +2245,7 @@
+ ALIAS 374833 n_meningitidis_053442
+ 
+ DBNAME n_meningitidis_2a [
++  comment: "SpeciesIdentifier=4"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/neisseria_collection_core_9_62_3a"
+@@ -2062,6 +2254,7 @@
+ ALIAS 272831 n_meningitidis_2a
+ 
+ DBNAME n_meningitidis_8013 [
++  comment: "SpeciesIdentifier=8"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/neisseria_collection_core_9_62_3a"
+@@ -2070,6 +2263,7 @@
+ ALIAS 604162 n_meningitidis_8013
+ 
+ DBNAME n_meningitidis_a [
++  comment: "SpeciesIdentifier=1"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/neisseria_collection_core_9_62_3a"
+@@ -2078,6 +2272,7 @@
+ ALIAS 122587 n_meningitidis_a
+ 
+ DBNAME n_meningitidis_alpha14 [
++  comment: "SpeciesIdentifier=7"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/neisseria_collection_core_9_62_3a"
+@@ -2086,6 +2281,7 @@
+ ALIAS 487 n_meningitidis_alpha14
+ 
+ DBNAME n_meningitidis_b [
++  comment: "SpeciesIdentifier=5"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/neisseria_collection_core_9_62_3a"
+@@ -2330,6 +2526,7 @@
+ ]
+ 
+ DBNAME p_abyssi [
++  comment: "SpeciesIdentifier=2"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/pyrococcus_collection_core_9_62_1a"
+@@ -2338,6 +2535,7 @@
+ ALIAS 272844 p_abyssi
+ 
+ DBNAME p_furiosus [
++  comment: "SpeciesIdentifier=3"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/pyrococcus_collection_core_9_62_1a"
+@@ -2346,6 +2544,7 @@
+ ALIAS 186497 p_furiosus
+ 
+ DBNAME p_horikoshii [
++  comment: "SpeciesIdentifier=1"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/pyrococcus_collection_core_9_62_1a"
+@@ -2354,6 +2553,7 @@
+ ALIAS 70601 p_horikoshii
+ 
+ DBNAME p_kodakaraensis [
++  comment: "SpeciesIdentifier=4"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/pyrococcus_collection_core_9_62_1a"
+@@ -2428,6 +2628,7 @@
+ ALIAS 7668 strongylocentrotus_purpuratus
+ 
+ DBNAME s_agalactiae_ia [
++  comment: "SpeciesIdentifier=3"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/streptococcus_collection_core_9_62_4a"
+@@ -2436,6 +2637,7 @@
+ ALIAS 205921 s_agalactiae_ia
+ 
+ DBNAME s_agalactiae_iii [
++  comment: "SpeciesIdentifier=2"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/streptococcus_collection_core_9_62_4a"
+@@ -2444,6 +2646,7 @@
+ ALIAS 211110 s_agalactiae_iii
+ 
+ DBNAME s_agalactiae_v [
++  comment: "SpeciesIdentifier=4"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/streptococcus_collection_core_9_62_4a"
+@@ -2452,6 +2655,7 @@
+ ALIAS 208435 s_agalactiae_v
+ 
+ DBNAME s_aureus_04_02981 [
++  comment: "SpeciesIdentifier=24"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_core_9_62_4a"
+@@ -2460,12 +2664,14 @@
+ ALIAS 703339 s_aureus_04_02981
+ 
+ DBNAME s_aureus_04_02981_funcgen [
++  comment: "SpeciesIdentifier=24"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_funcgen_9_62_4a"
+ ]
+ 
+ DBNAME s_aureus_bovine_rf122 [
++  comment: "SpeciesIdentifier=5"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_core_9_62_4a"
+@@ -2474,12 +2680,14 @@
+ ALIAS 273036 s_aureus_bovine_rf122
+ 
+ DBNAME s_aureus_bovine_rf122_funcgen [
++  comment: "SpeciesIdentifier=5"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_funcgen_9_62_4a"
+ ]
+ 
+ DBNAME s_aureus_col [
++  comment: "SpeciesIdentifier=4"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_core_9_62_4a"
+@@ -2488,12 +2696,14 @@
+ ALIAS 93062 s_aureus_col
+ 
+ DBNAME s_aureus_col_funcgen [
++  comment: "SpeciesIdentifier=4"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_funcgen_9_62_4a"
+ ]
+ 
+ DBNAME s_aureus_ed133 [
++  comment: "SpeciesIdentifier=25"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_core_9_62_4a"
+@@ -2502,12 +2712,14 @@
+ ALIAS 685039 s_aureus_ed133
+ 
+ DBNAME s_aureus_ed133_funcgen [
++  comment: "SpeciesIdentifier=25"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_funcgen_9_62_4a"
+ ]
+ 
+ DBNAME s_aureus_ed98 [
++  comment: "SpeciesIdentifier=21"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_core_9_62_4a"
+@@ -2516,12 +2728,14 @@
+ ALIAS 681288 s_aureus_ed98
+ 
+ DBNAME s_aureus_ed98_funcgen [
++  comment: "SpeciesIdentifier=21"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_funcgen_9_62_4a"
+ ]
+ 
+ DBNAME s_aureus_jh1 [
++  comment: "SpeciesIdentifier=6"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_core_9_62_4a"
+@@ -2530,12 +2744,14 @@
+ ALIAS 359787 s_aureus_jh1
+ 
+ DBNAME s_aureus_jh1_funcgen [
++  comment: "SpeciesIdentifier=6"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_funcgen_9_62_4a"
+ ]
+ 
+ DBNAME s_aureus_jh9 [
++  comment: "SpeciesIdentifier=7"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_core_9_62_4a"
+@@ -2544,12 +2760,14 @@
+ ALIAS 359786 s_aureus_jh9
+ 
+ DBNAME s_aureus_jh9_funcgen [
++  comment: "SpeciesIdentifier=7"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_funcgen_9_62_4a"
+ ]
+ 
+ DBNAME s_aureus_jkd6008 [
++  comment: "SpeciesIdentifier=26"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_core_9_62_4a"
+@@ -2558,12 +2776,14 @@
+ ALIAS 546342 s_aureus_jkd6008
+ 
+ DBNAME s_aureus_jkd6008_funcgen [
++  comment: "SpeciesIdentifier=26"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_funcgen_9_62_4a"
+ ]
+ 
+ DBNAME s_aureus_jkd6159 [
++  comment: "SpeciesIdentifier=23"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_core_9_62_4a"
+@@ -2572,12 +2792,14 @@
+ ALIAS 869816 s_aureus_jkd6159
+ 
+ DBNAME s_aureus_jkd6159_funcgen [
++  comment: "SpeciesIdentifier=23"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_funcgen_9_62_4a"
+ ]
+ 
+ DBNAME s_aureus_mrsa252 [
++  comment: "SpeciesIdentifier=8"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_core_9_62_4a"
+@@ -2586,12 +2808,14 @@
+ ALIAS 282458 s_aureus_mrsa252
+ 
+ DBNAME s_aureus_mrsa252_funcgen [
++  comment: "SpeciesIdentifier=8"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_funcgen_9_62_4a"
+ ]
+ 
+ DBNAME s_aureus_mssa476 [
++  comment: "SpeciesIdentifier=9"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_core_9_62_4a"
+@@ -2600,12 +2824,14 @@
+ ALIAS 282459 s_aureus_mssa476
+ 
+ DBNAME s_aureus_mssa476_funcgen [
++  comment: "SpeciesIdentifier=9"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_funcgen_9_62_4a"
+ ]
+ 
+ DBNAME s_aureus_mu3 [
++  comment: "SpeciesIdentifier=2"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_core_9_62_4a"
+@@ -2614,12 +2840,14 @@
+ ALIAS 418127 s_aureus_mu3
+ 
+ DBNAME s_aureus_mu3_funcgen [
++  comment: "SpeciesIdentifier=2"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_funcgen_9_62_4a"
+ ]
+ 
+ DBNAME s_aureus_mu50 [
++  comment: "SpeciesIdentifier=3"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_core_9_62_4a"
+@@ -2628,12 +2856,14 @@
+ ALIAS 158878 s_aureus_mu50
+ 
+ DBNAME s_aureus_mu50_funcgen [
++  comment: "SpeciesIdentifier=3"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_funcgen_9_62_4a"
+ ]
+ 
+ DBNAME s_aureus_mw2 [
++  comment: "SpeciesIdentifier=10"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_core_9_62_4a"
+@@ -2642,12 +2872,14 @@
+ ALIAS 196620 s_aureus_mw2
+ 
+ DBNAME s_aureus_mw2_funcgen [
++  comment: "SpeciesIdentifier=10"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_funcgen_9_62_4a"
+ ]
+ 
+ DBNAME s_aureus_n315 [
++  comment: "SpeciesIdentifier=1"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_core_9_62_4a"
+@@ -2656,12 +2888,14 @@
+ ALIAS 158879 s_aureus_n315
+ 
+ DBNAME s_aureus_n315_funcgen [
++  comment: "SpeciesIdentifier=1"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_funcgen_9_62_4a"
+ ]
+ 
+ DBNAME s_aureus_nctc_8325 [
++  comment: "SpeciesIdentifier=11"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_core_9_62_4a"
+@@ -2670,12 +2904,14 @@
+ ALIAS 93061 s_aureus_nctc_8325
+ 
+ DBNAME s_aureus_nctc_8325_funcgen [
++  comment: "SpeciesIdentifier=11"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_funcgen_9_62_4a"
+ ]
+ 
+ DBNAME s_aureus_newman [
++  comment: "SpeciesIdentifier=12"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_core_9_62_4a"
+@@ -2684,12 +2920,14 @@
+ ALIAS 426430 s_aureus_newman
+ 
+ DBNAME s_aureus_newman_funcgen [
++  comment: "SpeciesIdentifier=12"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_funcgen_9_62_4a"
+ ]
+ 
+ DBNAME s_aureus_st398 [
++  comment: "SpeciesIdentifier=20"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_core_9_62_4a"
+@@ -2698,12 +2936,14 @@
+ ALIAS 523796 s_aureus_st398
+ 
+ DBNAME s_aureus_st398_funcgen [
++  comment: "SpeciesIdentifier=20"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_funcgen_9_62_4a"
+ ]
+ 
+ DBNAME s_aureus_tch1516 [
++  comment: "SpeciesIdentifier=13"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_core_9_62_4a"
+@@ -2712,12 +2952,14 @@
+ ALIAS 451516 s_aureus_tch1516
+ 
+ DBNAME s_aureus_tch1516_funcgen [
++  comment: "SpeciesIdentifier=13"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_funcgen_9_62_4a"
+ ]
+ 
+ DBNAME s_aureus_tw20 [
++  comment: "SpeciesIdentifier=22"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_core_9_62_4a"
+@@ -2726,12 +2968,14 @@
+ ALIAS 663951 s_aureus_tw20
+ 
+ DBNAME s_aureus_tw20_funcgen [
++  comment: "SpeciesIdentifier=22"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_funcgen_9_62_4a"
+ ]
+ 
+ DBNAME s_aureus_usa300 [
++  comment: "SpeciesIdentifier=14"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_core_9_62_4a"
+@@ -2740,12 +2984,14 @@
+ ALIAS 451515 s_aureus_usa300
+ 
+ DBNAME s_aureus_usa300_funcgen [
++  comment: "SpeciesIdentifier=14"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_funcgen_9_62_4a"
+ ]
+ 
+ DBNAME s_boydii_18 [
++  comment: "SpeciesIdentifier=15"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_core_9_62_5a"
+@@ -2754,12 +3000,14 @@
+ ALIAS 344609 s_boydii_18
+ 
+ DBNAME s_boydii_18_funcgen [
++  comment: "SpeciesIdentifier=15"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_funcgen_9_62_5a"
+ ]
+ 
+ DBNAME s_boydii_4 [
++  comment: "SpeciesIdentifier=16"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_core_9_62_5a"
+@@ -2768,12 +3016,14 @@
+ ALIAS 300268 s_boydii_4
+ 
+ DBNAME s_boydii_4_funcgen [
++  comment: "SpeciesIdentifier=16"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_funcgen_9_62_5a"
+ ]
+ 
+ DBNAME s_carnosus [
++  comment: "SpeciesIdentifier=19"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_core_9_62_4a"
+@@ -2782,12 +3032,14 @@
+ ALIAS 396513 s_carnosus
+ 
+ DBNAME s_carnosus_funcgen [
++  comment: "SpeciesIdentifier=19"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_funcgen_9_62_4a"
+ ]
+ 
+ DBNAME s_dysenteriae [
++  comment: "SpeciesIdentifier=17"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_core_9_62_5a"
+@@ -2796,12 +3048,14 @@
+ ALIAS 300267 s_dysenteriae
+ 
+ DBNAME s_dysenteriae_funcgen [
++  comment: "SpeciesIdentifier=17"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_funcgen_9_62_5a"
+ ]
+ 
+ DBNAME s_dysgalactiae [
++  comment: "SpeciesIdentifier=40"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/streptococcus_collection_core_9_62_4a"
+@@ -2810,6 +3064,7 @@
+ ALIAS 486410 s_dysgalactiae
+ 
+ DBNAME s_epidermidis_atcc_12228 [
++  comment: "SpeciesIdentifier=15"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_core_9_62_4a"
+@@ -2818,12 +3073,14 @@
+ ALIAS 176280 s_epidermidis_atcc_12228
+ 
+ DBNAME s_epidermidis_atcc_12228_funcgen [
++  comment: "SpeciesIdentifier=15"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_funcgen_9_62_4a"
+ ]
+ 
+ DBNAME s_epidermidis_atcc_35984 [
++  comment: "SpeciesIdentifier=16"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_core_9_62_4a"
+@@ -2832,12 +3089,14 @@
+ ALIAS 176279 s_epidermidis_atcc_35984
+ 
+ DBNAME s_epidermidis_atcc_35984_funcgen [
++  comment: "SpeciesIdentifier=16"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_funcgen_9_62_4a"
+ ]
+ 
+ DBNAME s_equi [
++  comment: "SpeciesIdentifier=33"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/streptococcus_collection_core_9_62_4a"
+@@ -2846,6 +3105,7 @@
+ ALIAS 553482 s_equi
+ 
+ DBNAME s_equi_mgcs10565 [
++  comment: "SpeciesIdentifier=5"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/streptococcus_collection_core_9_62_4a"
+@@ -2854,6 +3114,7 @@
+ ALIAS 552526 s_equi_mgcs10565
+ 
+ DBNAME s_equi_zooepidemicus [
++  comment: "SpeciesIdentifier=32"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/streptococcus_collection_core_9_62_4a"
+@@ -2862,6 +3123,7 @@
+ ALIAS 40041 s_equi_zooepidemicus
+ 
+ DBNAME s_flexneri_2457t [
++  comment: "SpeciesIdentifier=18"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_core_9_62_5a"
+@@ -2870,12 +3132,14 @@
+ ALIAS 198215 s_flexneri_2457t
+ 
+ DBNAME s_flexneri_2457t_funcgen [
++  comment: "SpeciesIdentifier=18"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_funcgen_9_62_5a"
+ ]
+ 
+ DBNAME s_flexneri_301 [
++  comment: "SpeciesIdentifier=19"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_core_9_62_5a"
+@@ -2884,12 +3148,14 @@
+ ALIAS 198214 s_flexneri_301
+ 
+ DBNAME s_flexneri_301_funcgen [
++  comment: "SpeciesIdentifier=19"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_funcgen_9_62_5a"
+ ]
+ 
+ DBNAME s_flexneri_5b [
++  comment: "SpeciesIdentifier=20"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_core_9_62_5a"
+@@ -2898,12 +3164,14 @@
+ ALIAS 373384 s_flexneri_5b
+ 
+ DBNAME s_flexneri_5b_funcgen [
++  comment: "SpeciesIdentifier=20"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_funcgen_9_62_5a"
+ ]
+ 
+ DBNAME s_flexneri_x [
++  comment: "SpeciesIdentifier=41"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_core_9_62_5a"
+@@ -2912,12 +3180,14 @@
+ ALIAS 591020 s_flexneri_x
+ 
+ DBNAME s_flexneri_x_funcgen [
++  comment: "SpeciesIdentifier=41"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_funcgen_9_62_5a"
+ ]
+ 
+ DBNAME s_gallolyticus [
++  comment: "SpeciesIdentifier=45"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/streptococcus_collection_core_9_62_4a"
+@@ -2926,6 +3196,7 @@
+ ALIAS 637909 s_gallolyticus
+ 
+ DBNAME s_gordonii [
++  comment: "SpeciesIdentifier=6"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/streptococcus_collection_core_9_62_4a"
+@@ -2934,6 +3205,7 @@
+ ALIAS 467705 s_gordonii
+ 
+ DBNAME s_haemolyticus [
++  comment: "SpeciesIdentifier=17"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_core_9_62_4a"
+@@ -2942,12 +3214,14 @@
+ ALIAS 279808 s_haemolyticus
+ 
+ DBNAME s_haemolyticus_funcgen [
++  comment: "SpeciesIdentifier=17"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_funcgen_9_62_4a"
+ ]
+ 
+ DBNAME s_lugdunensis [
++  comment: "SpeciesIdentifier=27"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_core_9_62_4a"
+@@ -2956,12 +3230,14 @@
+ ALIAS 698737 s_lugdunensis
+ 
+ DBNAME s_lugdunensis_funcgen [
++  comment: "SpeciesIdentifier=27"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_funcgen_9_62_4a"
+ ]
+ 
+ DBNAME s_mitis [
++  comment: "SpeciesIdentifier=48"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/streptococcus_collection_core_9_62_4a"
+@@ -2970,6 +3246,7 @@
+ ALIAS 365659 s_mitis
+ 
+ DBNAME s_mutans_atcc_700610 [
++  comment: "SpeciesIdentifier=7"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/streptococcus_collection_core_9_62_4a"
+@@ -2978,6 +3255,7 @@
+ ALIAS 210007 s_mutans_atcc_700610
+ 
+ DBNAME s_mutans_nn2025 [
++  comment: "SpeciesIdentifier=44"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/streptococcus_collection_core_9_62_4a"
+@@ -2986,6 +3264,7 @@
+ ALIAS 511691 s_mutans_nn2025
+ 
+ DBNAME s_pneumoniae_70585 [
++  comment: "SpeciesIdentifier=34"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/streptococcus_collection_core_9_62_4a"
+@@ -2994,6 +3273,7 @@
+ ALIAS 488221 s_pneumoniae_70585
+ 
+ DBNAME s_pneumoniae_a19 [
++  comment: "SpeciesIdentifier=49"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/streptococcus_collection_core_9_62_4a"
+@@ -3002,6 +3282,7 @@
+ ALIAS 525381 s_pneumoniae_a19
+ 
+ DBNAME s_pneumoniae_atcc_700669 [
++  comment: "SpeciesIdentifier=39"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/streptococcus_collection_core_9_62_4a"
+@@ -3010,6 +3291,7 @@
+ ALIAS 561276 s_pneumoniae_atcc_700669
+ 
+ DBNAME s_pneumoniae_atcc_baa_255 [
++  comment: "SpeciesIdentifier=8"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/streptococcus_collection_core_9_62_4a"
+@@ -3018,6 +3300,7 @@
+ ALIAS 171101 s_pneumoniae_atcc_baa_255
+ 
+ DBNAME s_pneumoniae_cgsp14 [
++  comment: "SpeciesIdentifier=9"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/streptococcus_collection_core_9_62_4a"
+@@ -3026,6 +3309,7 @@
+ ALIAS 516950 s_pneumoniae_cgsp14
+ 
+ DBNAME s_pneumoniae_d39 [
++  comment: "SpeciesIdentifier=10"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/streptococcus_collection_core_9_62_4a"
+@@ -3034,6 +3318,7 @@
+ ALIAS 373153 s_pneumoniae_d39
+ 
+ DBNAME s_pneumoniae_g54 [
++  comment: "SpeciesIdentifier=11"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/streptococcus_collection_core_9_62_4a"
+@@ -3042,6 +3327,7 @@
+ ALIAS 512566 s_pneumoniae_g54
+ 
+ DBNAME s_pneumoniae_hungary19a_6 [
++  comment: "SpeciesIdentifier=12"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/streptococcus_collection_core_9_62_4a"
+@@ -3050,6 +3336,7 @@
+ ALIAS 487214 s_pneumoniae_hungary19a_6
+ 
+ DBNAME s_pneumoniae_jja [
++  comment: "SpeciesIdentifier=35"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/streptococcus_collection_core_9_62_4a"
+@@ -3058,6 +3345,7 @@
+ ALIAS 488222 s_pneumoniae_jja
+ 
+ DBNAME s_pneumoniae_p1031 [
++  comment: "SpeciesIdentifier=37"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/streptococcus_collection_core_9_62_4a"
+@@ -3066,6 +3354,7 @@
+ ALIAS 488223 s_pneumoniae_p1031
+ 
+ DBNAME s_pneumoniae_taiwan19f_14 [
++  comment: "SpeciesIdentifier=36"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/streptococcus_collection_core_9_62_4a"
+@@ -3074,6 +3363,7 @@
+ ALIAS 487213 s_pneumoniae_taiwan19f_14
+ 
+ DBNAME s_pneumoniae_tigr4 [
++  comment: "SpeciesIdentifier=13"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/streptococcus_collection_core_9_62_4a"
+@@ -3082,6 +3372,7 @@
+ ALIAS 170187 s_pneumoniae_tigr4
+ 
+ DBNAME s_pyogenes_atcc_baa_595 [
++  comment: "SpeciesIdentifier=17"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/streptococcus_collection_core_9_62_4a"
+@@ -3090,6 +3381,7 @@
+ ALIAS 198466 s_pyogenes_atcc_baa_595
+ 
+ DBNAME s_pyogenes_m18 [
++  comment: "SpeciesIdentifier=15"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/streptococcus_collection_core_9_62_4a"
+@@ -3098,6 +3390,7 @@
+ ALIAS 186103 s_pyogenes_m18
+ 
+ DBNAME s_pyogenes_m2 [
++  comment: "SpeciesIdentifier=20"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/streptococcus_collection_core_9_62_4a"
+@@ -3106,6 +3399,7 @@
+ ALIAS 370552 s_pyogenes_m2
+ 
+ DBNAME s_pyogenes_m28 [
++  comment: "SpeciesIdentifier=16"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/streptococcus_collection_core_9_62_4a"
+@@ -3114,6 +3408,7 @@
+ ALIAS 319701 s_pyogenes_m28
+ 
+ DBNAME s_pyogenes_m4 [
++  comment: "SpeciesIdentifier=21"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/streptococcus_collection_core_9_62_4a"
+@@ -3122,6 +3417,7 @@
+ ALIAS 370554 s_pyogenes_m4
+ 
+ DBNAME s_pyogenes_m49 [
++  comment: "SpeciesIdentifier=25"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/streptococcus_collection_core_9_62_4a"
+@@ -3130,6 +3426,7 @@
+ ALIAS 471876 s_pyogenes_m49
+ 
+ DBNAME s_pyogenes_m5 [
++  comment: "SpeciesIdentifier=24"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/streptococcus_collection_core_9_62_4a"
+@@ -3138,6 +3435,7 @@
+ ALIAS 160491 s_pyogenes_m5
+ 
+ DBNAME s_pyogenes_m6 [
++  comment: "SpeciesIdentifier=19"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/streptococcus_collection_core_9_62_4a"
+@@ -3146,6 +3444,7 @@
+ ALIAS 286636 s_pyogenes_m6
+ 
+ DBNAME s_pyogenes_mgas2096 [
++  comment: "SpeciesIdentifier=22"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/streptococcus_collection_core_9_62_4a"
+@@ -3154,6 +3453,7 @@
+ ALIAS 370553 s_pyogenes_mgas2096
+ 
+ DBNAME s_pyogenes_mgas5005 [
++  comment: "SpeciesIdentifier=14"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/streptococcus_collection_core_9_62_4a"
+@@ -3162,6 +3462,7 @@
+ ALIAS 293653 s_pyogenes_mgas5005
+ 
+ DBNAME s_pyogenes_mgas9429 [
++  comment: "SpeciesIdentifier=23"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/streptococcus_collection_core_9_62_4a"
+@@ -3170,6 +3471,7 @@
+ ALIAS 370551 s_pyogenes_mgas9429
+ 
+ DBNAME s_pyogenes_sf370 [
++  comment: "SpeciesIdentifier=1"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/streptococcus_collection_core_9_62_4a"
+@@ -3178,6 +3480,7 @@
+ ALIAS 160490 s_pyogenes_sf370
+ 
+ DBNAME s_pyogenes_ssi_1 [
++  comment: "SpeciesIdentifier=18"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/streptococcus_collection_core_9_62_4a"
+@@ -3186,6 +3489,7 @@
+ ALIAS 193567 s_pyogenes_ssi_1
+ 
+ DBNAME s_sanguinis [
++  comment: "SpeciesIdentifier=26"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/streptococcus_collection_core_9_62_4a"
+@@ -3194,6 +3498,7 @@
+ ALIAS 388919 s_sanguinis
+ 
+ DBNAME s_saprophyticus [
++  comment: "SpeciesIdentifier=18"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_core_9_62_4a"
+@@ -3202,12 +3507,14 @@
+ ALIAS 342451 s_saprophyticus
+ 
+ DBNAME s_saprophyticus_funcgen [
++  comment: "SpeciesIdentifier=18"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/staphylococcus_collection_funcgen_9_62_4a"
+ ]
+ 
+ DBNAME s_sonnei [
++  comment: "SpeciesIdentifier=21"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_core_9_62_5a"
+@@ -3216,12 +3523,14 @@
+ ALIAS 300269 s_sonnei
+ 
+ DBNAME s_sonnei_funcgen [
++  comment: "SpeciesIdentifier=21"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/escherichia_shigella_collection_funcgen_9_62_5a"
+ ]
+ 
+ DBNAME s_suis_05zyh33 [
++  comment: "SpeciesIdentifier=27"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/streptococcus_collection_core_9_62_4a"
+@@ -3230,6 +3539,7 @@
+ ALIAS 391295 s_suis_05zyh33
+ 
+ DBNAME s_suis_98hah33 [
++  comment: "SpeciesIdentifier=28"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/streptococcus_collection_core_9_62_4a"
+@@ -3238,6 +3548,7 @@
+ ALIAS 391296 s_suis_98hah33
+ 
+ DBNAME s_suis_bm407 [
++  comment: "SpeciesIdentifier=42"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/streptococcus_collection_core_9_62_4a"
+@@ -3246,6 +3557,7 @@
+ ALIAS 568814 s_suis_bm407
+ 
+ DBNAME s_suis_gz1 [
++  comment: "SpeciesIdentifier=50"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/streptococcus_collection_core_9_62_4a"
+@@ -3254,6 +3566,7 @@
+ ALIAS 423211 s_suis_gz1
+ 
+ DBNAME s_suis_p1_7 [
++  comment: "SpeciesIdentifier=43"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/streptococcus_collection_core_9_62_4a"
+@@ -3262,6 +3575,7 @@
+ ALIAS 218494 s_suis_p1_7
+ 
+ DBNAME s_suis_sc84 [
++  comment: "SpeciesIdentifier=41"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/streptococcus_collection_core_9_62_4a"
+@@ -3270,6 +3584,7 @@
+ ALIAS 568813 s_suis_sc84
+ 
+ DBNAME s_thermophilus_atcc_baa_250 [
++  comment: "SpeciesIdentifier=29"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/streptococcus_collection_core_9_62_4a"
+@@ -3278,6 +3593,7 @@
+ ALIAS 264199 s_thermophilus_atcc_baa_250
+ 
+ DBNAME s_thermophilus_atcc_baa_491 [
++  comment: "SpeciesIdentifier=30"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/streptococcus_collection_core_9_62_4a"
+@@ -3286,6 +3602,7 @@
+ ALIAS 322159 s_thermophilus_atcc_baa_491
+ 
+ DBNAME s_thermophilus_cnrz_1066 [
++  comment: "SpeciesIdentifier=31"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/streptococcus_collection_core_9_62_4a"
+@@ -3294,6 +3611,7 @@
+ ALIAS 299768 s_thermophilus_cnrz_1066
+ 
+ DBNAME s_uberis [
++  comment: "SpeciesIdentifier=38"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/streptococcus_collection_core_9_62_4a"
+@@ -3350,6 +3668,7 @@
+ ]
+ 
+ DBNAME wolbachia_sp_brugia_malayi [
++  comment: "SpeciesIdentifier=3"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/wolbachia_collection_core_9_62_1a"
+@@ -3358,6 +3677,7 @@
+ ALIAS 292805 wolbachia_sp_brugia_malayi
+ 
+ DBNAME wolbachia_sp_drosophila_simulans [
++  comment: "SpeciesIdentifier=2"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/wolbachia_collection_core_9_62_1a"
+@@ -3366,6 +3686,7 @@
+ ALIAS 66084 wolbachia_sp_drosophila_simulans
+ 
+ DBNAME w_pipientis_culex_pipiens [
++  comment: "SpeciesIdentifier=1"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/wolbachia_collection_core_9_62_1a"
+@@ -3374,6 +3695,7 @@
+ ALIAS 570417 w_pipientis_culex_pipiens
+ 
+ DBNAME w_pipientis_wmel [
++  comment: "SpeciesIdentifier=4"
+   release: "62"
+   server:  "ensemblgenomes"
+   url:     "mysql://anonymous@mysql.ebi.ac.uk:4157/wolbachia_collection_core_9_62_1a"
+--- emboss-6.4.0.orig/nucleus/embgroup.c
++++ emboss-6.4.0/nucleus/embgroup.c
+@@ -1173,7 +1173,7 @@
+     AjPStr tail;
+     AjPStr revhead;
+     AjPStr revtail;
+-    AjPStr dummy;		 /* dummy string for ajListstrPop() */
++    AjPStr dummy = NULL;        /* dummy string for ajListstrPop() */
+ 
+ 
+     len = ajListstrToarray(sublist, &sub);
--- emboss-6.4.0.orig/debian/manpages/drtext.1e
+++ emboss-6.4.0/debian/manpages/drtext.1e
@@ -0,0 +1,72 @@
+'\" t
+.\"     Title: DRTEXT
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "DRTEXT" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+drtext \- Get data resource entries complete text
+.SH "SYNOPSIS"
+.HP \w'\fBdrtext\fR\ 'u
+\fBdrtext\fR \fB\-resources\ \fR\fB\fIresource\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBdrtext\fR\ 'u
+\fBdrtext\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBdrtext\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Data retrieval:Resource data,Data retrieval:Text data" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-resources\fR \fIresource\fR
+.RS 4
+.RE
+.SS "Additional section"
+.SS "Advanced section"
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+drtext is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/corbatest.1e
+++ emboss-6.4.0/debian/manpages/corbatest.1e
@@ -0,0 +1,71 @@
+'\" t
+.\"     Title: CORBATEST
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "CORBATEST" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+corbatest \- Test of EMBL corba retrieval
+.SH "SYNOPSIS"
+.HP \w'\fBcorbatest\fR\ 'u
+\fBcorbatest\fR \fB\-entry\ \fR\fB\fIstring\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBcorbatest\fR\ 'u
+\fBcorbatest\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBcorbatest\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Test" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-entry\fR \fIstring\fR
+.RS 4
+Default value: hsfau
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+corbatest is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/supermatcher.1e
+++ emboss-6.4.0/debian/manpages/supermatcher.1e
@@ -0,0 +1,111 @@
+'\" t
+.\"     Title: SUPERMATCHER
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "SUPERMATCHER" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+supermatcher \- Calculate approximate local pair\-wise alignments of larger sequences
+.SH "SYNOPSIS"
+.HP \w'\fBsupermatcher\fR\ 'u
+\fBsupermatcher\fR \fB\-asequence\ \fR\fB\fIseqall\fR\fR \fB\-bsequence\ \fR\fB\fIseqset\fR\fR [\fB\-datafile\ \fR\fB\fImatrixf\fR\fR] [\fB\-minscore\ \fR\fB\fIfloat\fR\fR] \fB\-gapopen\ \fR\fB\fIfloat\fR\fR \fB\-gapextend\ \fR\fB\fIfloat\fR\fR [\fB\-width\ \fR\fB\fIinteger\fR\fR] [\fB\-wordlen\ \fR\fB\fIinteger\fR\fR] \fB\-outfile\ \fR\fB\fIalign\fR\fR [\fB\-errorfile\ \fR\fB\fIoutfile\fR\fR]
+.HP \w'\fBsupermatcher\fR\ 'u
+\fBsupermatcher\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBsupermatcher\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Alignment:Local" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-asequence\fR \fIseqall\fR
+.RS 4
+.RE
+.PP
+\fB\-bsequence\fR \fIseqset\fR
+.RS 4
+.RE
+.PP
+\fB\-datafile\fR \fImatrixf\fR
+.RS 4
+This is the scoring matrix file used when comparing sequences\&. By default it is the file \*(AqEBLOSUM62\*(Aq (for proteins) or the file \*(AqEDNAFULL\*(Aq (for nucleic sequences)\&. These files are found in the \*(Aqdata\*(Aq directory of the EMBOSS installation\&.
+.RE
+.PP
+\fB\-minscore\fR \fIfloat\fR
+.RS 4
+Minimum alignment score to report an alignment\&.
+.RE
+.SS "Required section"
+.PP
+\fB\-gapopen\fR \fIfloat\fR
+.RS 4
+Default value: @($(acdprotein)? 10\&.0 : 10\&.0)
+.RE
+.PP
+\fB\-gapextend\fR \fIfloat\fR
+.RS 4
+Default value: @($(acdprotein)? 0\&.5 : 0\&.5)
+.RE
+.SS "Additional section"
+.PP
+\fB\-width\fR \fIinteger\fR
+.RS 4
+Default value: 16
+.RE
+.PP
+\fB\-wordlen\fR \fIinteger\fR
+.RS 4
+Default value: 6
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIalign\fR
+.RS 4
+.RE
+.PP
+\fB\-errorfile\fR \fIoutfile\fR
+.RS 4
+Error file to be written to for failed alignments Default value: supermatcher\&.error
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+supermatcher is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/wossdata.1e
+++ emboss-6.4.0/debian/manpages/wossdata.1e
@@ -0,0 +1,139 @@
+'\" t
+.\"     Title: WOSSDATA
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "WOSSDATA" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+wossdata \- Finds programs by EDAM data
+.SH "SYNOPSIS"
+.HP \w'\fBwossdata\fR\ 'u
+\fBwossdata\fR \fB\-identifier\ \fR\fB\fIstring\fR\fR [\fB\-explode\ \fR\fB\fIboolean\fR\fR] [\fB\-showkeywords\ \fR\fB\fIboolean\fR\fR] \fB\-sensitive\ \fR\fB\fIboolean\fR\fR \fB\-subclasses\ \fR\fB\fIboolean\fR\fR \fB\-obsolete\ \fR\fB\fIboolean\fR\fR \fB\-emboss\ \fR\fB\fIboolean\fR\fR \fB\-embassy\ \fR\fB\fIboolean\fR\fR \fB\-showembassy\ \fR\fB\fIstring\fR\fR \fB\-colon\ \fR\fB\fIboolean\fR\fR \fB\-gui\ \fR\fB\fIboolean\fR\fR [\fB\-outfile\ \fR\fB\fIoutfile\fR\fR] [\fB\-html\ \fR\fB\fItoggle\fR\fR] [\fB\-groups\ \fR\fB\fIboolean\fR\fR] [\fB\-alphabetic\ \fR\fB\fIboolean\fR\fR]
+.HP \w'\fBwossdata\fR\ 'u
+\fBwossdata\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBwossdata\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Ontology:EDAM,Documentation" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-identifier\fR \fIstring\fR
+.RS 4
+.RE
+.SS "Additional section"
+.PP
+\fB\-explode\fR \fIboolean\fR
+.RS 4
+The groups that EMBOSS applications belong to have two forms, exploded and not exploded\&. The exploded group names are more numerous and often vaguely phrased than the non\-exploded ones\&. The exploded names are formed from definitions of the group names that start like NAME1:NAME2 and which are then expanded into many combinations of the names as: \*(AqNAME1\*(Aq, \*(AqNAME2\*(Aq, \*(AqNAME1 NAME2\*(Aq, NAME2 NAME1\*(Aq\&. The non\-expanded names are simply like: \*(AqNAME1 NAME2\*(Aq\&. Default value: N
+.RE
+.PP
+\fB\-showkeywords\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.SS "Advanced section"
+.PP
+\fB\-sensitive\fR \fIboolean\fR
+.RS 4
+By default, the query keywords are matched against the EDAM term names (and synonyms) only\&. This option also matches the keywords against the EDAM term definitions and will therefore (typically) report more matches\&. Default value: N
+.RE
+.PP
+\fB\-subclasses\fR \fIboolean\fR
+.RS 4
+Extend the query matches to include all terms which are specialisations (EDAM sub\-classes) of the matched type\&. Default value: Y
+.RE
+.PP
+\fB\-obsolete\fR \fIboolean\fR
+.RS 4
+The default behaviour is to not use or return obsolete terms\&. This option if set will include all terms\&. Default value: N
+.RE
+.PP
+\fB\-emboss\fR \fIboolean\fR
+.RS 4
+If you use this option then EMBOSS program documentation will be searched\&. If this option is set to be false, then only the EMBASSY programs will be searched (if the \-embassy option is true)\&. EMBASSY programs are not strictly part of EMBOSS, but use the same code libraries and share the same look and feel, but are generally developed by people who wish the programs to be outside of the GNU Public Licence scheme Default value: Y
+.RE
+.PP
+\fB\-embassy\fR \fIboolean\fR
+.RS 4
+If you use this option then EMBASSY program documentation will be searched\&. If this option is set to be false, then only the EMBOSS programs will be searched (if the \-emboss option is true)\&. EMBASSY programs are not strictly part of EMBOSS, but use the same code libraries and share the same look and feel, but are generally developed by people who wish the programs to be outside of the GNU Public Licence scheme Default value: Y
+.RE
+.PP
+\fB\-showembassy\fR \fIstring\fR
+.RS 4
+If you use this option then this EMBASSY package program documentation will be searched\&. EMBASSY programs are not strictly part of EMBOSS, but use the same code libraries and share the same look and feel, but are generally developed by people who wish the programs to be outside of the GNU Public Licence scheme
+.RE
+.PP
+\fB\-colon\fR \fIboolean\fR
+.RS 4
+The groups that EMBOSS applications belong to up to two levels, for example the primary group \*(AqALIGNMENT\*(Aq has several sub\-groups, or second\-level groups, e\&.g\&.: CONSENSUS, DIFFERENCES, DOT PLOTS, GLOBAL, LOCAL, MULTIPLE\&. To aid programs that parse the output of wossname that require the names of these subgroups, a colon \*(Aq:\*(Aq will be placed between the first and second level of the group name if this option is true\&. Note: This does not apply if the group names have been exploded with the \*(Aqexplode\*(Aq option\&. Default value: N
+.RE
+.PP
+\fB\-gui\fR \fIboolean\fR
+.RS 4
+This option is intended to help those who are designing Graphical User Interfaces to the EMBOSS applications\&. Some EMBOSS programs are inappropriate for running in a GUI, these include other menu programs and interactive editors\&. This option allows you to only report those programs that can be run from a GUI Default value: N
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+Default value: stdout
+.RE
+.SS "Html section"
+.PP
+\fB\-html\fR \fItoggle\fR
+.RS 4
+If you are sending the output to a file, this will format it for displaying as a table in a WWW document\&. Default value: N
+.RE
+.PP
+\fB\-groups\fR \fIboolean\fR
+.RS 4
+If you use this option, then only the group names will be output to the file Default value: N
+.RE
+.PP
+\fB\-alphabetic\fR \fIboolean\fR
+.RS 4
+If you use this option, then you will get a single list of the program names and descriptions instead of the programs being listed in their functional groups\&. Default value: N
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+wossdata is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/prophecy.1e
+++ emboss-6.4.0/debian/manpages/prophecy.1e
@@ -0,0 +1,103 @@
+'\" t
+.\"     Title: PROPHECY
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "PROPHECY" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+prophecy \- Create frequency matrix or profile from a multiple alignment
+.SH "SYNOPSIS"
+.HP \w'\fBprophecy\fR\ 'u
+\fBprophecy\fR \fB\-sequence\ \fR\fB\fIseqset\fR\fR \fB\-type\ \fR\fB\fIlist\fR\fR \fB\-datafile\ \fR\fB\fImatrixf\fR\fR \fB\-name\ \fR\fB\fIstring\fR\fR \fB\-threshold\ \fR\fB\fIinteger\fR\fR \fB\-open\ \fR\fB\fIfloat\fR\fR \fB\-extension\ \fR\fB\fIfloat\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBprophecy\fR\ 'u
+\fBprophecy\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBprophecy\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Profiles,Protein:Profiles" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqset\fR
+.RS 4
+.RE
+.PP
+\fB\-type\fR \fIlist\fR
+.RS 4
+Default value: F
+.RE
+.PP
+\fB\-datafile\fR \fImatrixf\fR
+.RS 4
+Default value: @($(type) = G: Epprofile H: EBLOSUM62 F: EBLOSUM62)
+.RE
+.SS "Required section"
+.PP
+\fB\-name\fR \fIstring\fR
+.RS 4
+Default value: mymatrix
+.RE
+.SS "Profile type specific options"
+.PP
+\fB\-threshold\fR \fIinteger\fR
+.RS 4
+Default value: 75
+.RE
+.SS "Gap options"
+.PP
+\fB\-open\fR \fIfloat\fR
+.RS 4
+Default value: 3\&.0
+.RE
+.PP
+\fB\-extension\fR \fIfloat\fR
+.RS 4
+Default value: 0\&.3
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+prophecy is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/seqxrefget.1e
+++ emboss-6.4.0/debian/manpages/seqxrefget.1e
@@ -0,0 +1,73 @@
+'\" t
+.\"     Title: SEQXREFGET
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "SEQXREFGET" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+seqxrefget \- Retrieve all cross\-referenced data for a sequence entry
+.SH "SYNOPSIS"
+.HP \w'\fBseqxrefget\fR\ 'u
+\fBseqxrefget\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBseqxrefget\fR\ 'u
+\fBseqxrefget\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBseqxrefget\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Data retrieval:Sequence data" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqall\fR
+.RS 4
+.RE
+.SS "Required section"
+.SS "Additional section"
+.SS "Advanced section"
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+seqxrefget is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/newcpgseek.1e
+++ emboss-6.4.0/debian/manpages/newcpgseek.1e
@@ -0,0 +1,76 @@
+'\" t
+.\"     Title: NEWCPGSEEK
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "NEWCPGSEEK" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+newcpgseek \- Identify and report CpG\-rich regions in nucleotide sequence(s)
+.SH "SYNOPSIS"
+.HP \w'\fBnewcpgseek\fR\ 'u
+\fBnewcpgseek\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-score\ \fR\fB\fIinteger\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBnewcpgseek\fR\ 'u
+\fBnewcpgseek\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBnewcpgseek\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:CpG Islands" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqall\fR
+.RS 4
+.RE
+.SS "Required section"
+.PP
+\fB\-score\fR \fIinteger\fR
+.RS 4
+Default value: 17
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+newcpgseek is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/edamname.1e
+++ emboss-6.4.0/debian/manpages/edamname.1e
@@ -0,0 +1,87 @@
+'\" t
+.\"     Title: EDAMNAME
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "EDAMNAME" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+edamname \- Find EDAM ontology terms by name
+.SH "SYNOPSIS"
+.HP \w'\fBedamname\fR\ 'u
+\fBedamname\fR \fB\-query\ \fR\fB\fIstring\fR\fR [\fB\-namespace\ \fR\fB\fIlist\fR\fR] \fB\-subclasses\ \fR\fB\fIboolean\fR\fR \fB\-obsolete\ \fR\fB\fIboolean\fR\fR \fB\-edamname\ \fR\fB\fIoutobo\fR\fR
+.HP \w'\fBedamname\fR\ 'u
+\fBedamname\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBedamname\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Ontology:EDAM,Data retrieval:Ontology data" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-query\fR \fIstring\fR
+.RS 4
+.RE
+.SS "Additional section"
+.PP
+\fB\-namespace\fR \fIlist\fR
+.RS 4
+By default all terms are returned\&. Searches can be limited to one or a few namespaces\&. Default value: *
+.RE
+.SS "Advanced section"
+.PP
+\fB\-subclasses\fR \fIboolean\fR
+.RS 4
+Extend the query matches to include all terms which are specialisations (EDAM sub\-classes) of the matched type\&. Default value: N
+.RE
+.PP
+\fB\-obsolete\fR \fIboolean\fR
+.RS 4
+The default behaviour is to not use or return obsolete terms\&. This option if set will include all terms\&. Default value: N
+.RE
+.SS "Output section"
+.PP
+\fB\-edamname\fR \fIoutobo\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+edamname is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/domtestd.1e
+++ emboss-6.4.0/debian/manpages/domtestd.1e
@@ -0,0 +1,65 @@
+'\" t
+.\"     Title: DOMTESTD
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "DOMTESTD" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+domtestd \- Create some XML and search for an element
+.SH "SYNOPSIS"
+.HP \w'\fBdomtestd\fR\ 'u
+\fBdomtestd\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBdomtestd\fR\ 'u
+\fBdomtestd\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBdomtestd\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&.
+.SH "OPTIONS"
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+domtestd is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/sizeseq.1e
+++ emboss-6.4.0/debian/manpages/sizeseq.1e
@@ -0,0 +1,83 @@
+'\" t
+.\"     Title: SIZESEQ
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "SIZESEQ" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+sizeseq \- Sort sequences by size
+.SH "SYNOPSIS"
+.HP \w'\fBsizeseq\fR\ 'u
+\fBsizeseq\fR \fB\-feature\ \fR\fB\fIboolean\fR\fR \fB\-sequences\ \fR\fB\fIseqset\fR\fR \fB\-descending\ \fR\fB\fIboolean\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR
+.HP \w'\fBsizeseq\fR\ 'u
+\fBsizeseq\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBsizeseq\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-feature\fR \fIboolean\fR
+.RS 4
+Sequence feature information will be retained if this option is set\&.
+.RE
+.PP
+\fB\-sequences\fR \fIseqset\fR
+.RS 4
+.RE
+.SS "Required section"
+.PP
+\fB\-descending\fR \fIboolean\fR
+.RS 4
+By default the shortest sequence is given first\&. Default value: N
+.RE
+.SS "Additional section"
+.SS "Advanced section"
+.SS "Output section"
+.PP
+\fB\-outseq\fR \fIseqoutall\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+sizeseq is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/dbxresource.1e
+++ emboss-6.4.0/debian/manpages/dbxresource.1e
@@ -0,0 +1,122 @@
+'\" t
+.\"     Title: DBXRESOURCE
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "DBXRESOURCE" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+dbxresource \- Index a data resource catalogue using b+tree indices
+.SH "SYNOPSIS"
+.HP \w'\fBdbxresource\fR\ 'u
+\fBdbxresource\fR \fB\-dbname\ \fR\fB\fIstring\fR\fR \fB\-standardname\ \fR\fB\fIstring\fR\fR \fB\-dbresource\ \fR\fB\fIstring\fR\fR \fB\-directory\ \fR\fB\fIdirectory\fR\fR \fB\-filenames\ \fR\fB\fIstring\fR\fR \fB\-fields\ \fR\fB\fIlist\fR\fR \fB\-compressed\ \fR\fB\fIboolean\fR\fR \fB\-release\ \fR\fB\fIstring\fR\fR \fB\-date\ \fR\fB\fIstring\fR\fR \fB\-exclude\ \fR\fB\fIstring\fR\fR \fB\-indexoutdir\ \fR\fB\fIoutdir\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBdbxresource\fR\ 'u
+\fBdbxresource\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBdbxresource\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Database indexing" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-dbname\fR \fIstring\fR
+.RS 4
+Default value: drcat
+.RE
+.PP
+\fB\-standardname\fR \fIstring\fR
+.RS 4
+Default value: $(dbname)
+.RE
+.PP
+\fB\-dbresource\fR \fIstring\fR
+.RS 4
+Default value: drcatresource
+.RE
+.PP
+\fB\-directory\fR \fIdirectory\fR
+.RS 4
+Default value: \&.
+.RE
+.PP
+\fB\-filenames\fR \fIstring\fR
+.RS 4
+Default value: DRCAT\&.dat
+.RE
+.SS "Required section"
+.PP
+\fB\-fields\fR \fIlist\fR
+.RS 4
+Default value: *
+.RE
+.PP
+\fB\-compressed\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.SS "Advanced section"
+.PP
+\fB\-release\fR \fIstring\fR
+.RS 4
+Default value: 0\&.0
+.RE
+.PP
+\fB\-date\fR \fIstring\fR
+.RS 4
+Default value: 00/00/00
+.RE
+.PP
+\fB\-exclude\fR \fIstring\fR
+.RS 4
+.RE
+.SS "Output section"
+.PP
+\fB\-indexoutdir\fR \fIoutdir\fR
+.RS 4
+Default value: \&.
+.RE
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+dbxresource is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/docxmlwell.1e
+++ emboss-6.4.0/debian/manpages/docxmlwell.1e
@@ -0,0 +1,73 @@
+'\" t
+.\"     Title: DOCXMLWELL
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "DOCXMLWELL" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+docxmlwell \- Check an XML document is well formed
+.SH "SYNOPSIS"
+.HP \w'\fBdocxmlwell\fR\ 'u
+\fBdocxmlwell\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR \fB\-logfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBdocxmlwell\fR\ 'u
+\fBdocxmlwell\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBdocxmlwell\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Misc" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-infile\fR \fIinfile\fR
+.RS 4
+.RE
+.SS "Required section"
+.SS "Additional section"
+.SS "Advanced section"
+.SS "Output section"
+.PP
+\fB\-logfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+docxmlwell is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/nthseq.1e
+++ emboss-6.4.0/debian/manpages/nthseq.1e
@@ -0,0 +1,76 @@
+'\" t
+.\"     Title: NTHSEQ
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "NTHSEQ" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+nthseq \- Write to file a single sequence from an input stream of sequences
+.SH "SYNOPSIS"
+.HP \w'\fBnthseq\fR\ 'u
+\fBnthseq\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-number\ \fR\fB\fIinteger\fR\fR \fB\-outseq\ \fR\fB\fIseqout\fR\fR
+.HP \w'\fBnthseq\fR\ 'u
+\fBnthseq\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBnthseq\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqall\fR
+.RS 4
+.RE
+.SS "Required section"
+.PP
+\fB\-number\fR \fIinteger\fR
+.RS 4
+Default value: 1
+.RE
+.SS "Output section"
+.PP
+\fB\-outseq\fR \fIseqout\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+nthseq is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/martfilters.1e
+++ emboss-6.4.0/debian/manpages/martfilters.1e
@@ -0,0 +1,87 @@
+'\" t
+.\"     Title: MARTFILTERS
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "MARTFILTERS" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+martfilters \- Return filters from a mart dataset from a mart host
+.SH "SYNOPSIS"
+.HP \w'\fBmartfilters\fR\ 'u
+\fBmartfilters\fR \fB\-dataset\ \fR\fB\fIstring\fR\fR \fB\-host\ \fR\fB\fIstring\fR\fR \fB\-path\ \fR\fB\fIstring\fR\fR \fB\-port\ \fR\fB\fIinteger\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBmartfilters\fR\ 'u
+\fBmartfilters\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBmartfilters\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-dataset\fR \fIstring\fR
+.RS 4
+Default value: oanatinus_gene_ensembl
+.RE
+.SS "Advanced section"
+.PP
+\fB\-host\fR \fIstring\fR
+.RS 4
+Default value: www\&.biomart\&.org
+.RE
+.PP
+\fB\-path\fR \fIstring\fR
+.RS 4
+Default value: /biomart/martservice
+.RE
+.PP
+\fB\-port\fR \fIinteger\fR
+.RS 4
+Default value: 80
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+martfilters is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/acdc.1e
+++ emboss-6.4.0/debian/manpages/acdc.1e
@@ -0,0 +1,60 @@
+'\" t
+.\"     Title: ACDC
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "ACDC" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+acdc \- Test an application ACD file
+.SH "SYNOPSIS"
+.HP \w'\fBacdc\fR\ 'u
+\fBacdc\fR
+.HP \w'\fBacdc\fR\ 'u
+\fBacdc\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBacdc\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Acd,Data retrieval:Tool data" command group(s)\&.
+.SH "OPTIONS"
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+acdc is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/tcode.1e
+++ emboss-6.4.0/debian/manpages/tcode.1e
@@ -0,0 +1,96 @@
+'\" t
+.\"     Title: TCODE
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "TCODE" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+tcode \- Identify protein\-coding regions using Fickett TESTCODE statistic
+.SH "SYNOPSIS"
+.HP \w'\fBtcode\fR\ 'u
+\fBtcode\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-datafile\ \fR\fB\fIdatafile\fR\fR \fB\-window\ \fR\fB\fIinteger\fR\fR \fB\-step\ \fR\fB\fIinteger\fR\fR \fB\-plot\ \fR\fB\fItoggle\fR\fR \fB\-outfile\ \fR\fB\fIreport\fR\fR \fB\-graph\ \fR\fB\fIxygraph\fR\fR
+.HP \w'\fBtcode\fR\ 'u
+\fBtcode\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBtcode\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Gene finding" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqall\fR
+.RS 4
+.RE
+.PP
+\fB\-datafile\fR \fIdatafile\fR
+.RS 4
+The default data file is Etcode\&.dat and contains coding probabilities for each base\&. The probabilities are for both positional and compositional information\&. Default value: Etcode\&.dat
+.RE
+.SS "Required section"
+.PP
+\fB\-window\fR \fIinteger\fR
+.RS 4
+This is the number of nucleotide bases over which the TESTCODE statistic will be performed each time\&. The window will then slide along the sequence, covering the same number of bases each time\&. Default value: 200
+.RE
+.SS "Advanced section"
+.PP
+\fB\-step\fR \fIinteger\fR
+.RS 4
+The selected window will, by default, slide along the nucleotide sequence by three bases at a time, retaining the frame (although the algorithm is not frame sensitive)\&. This may be altered to increase or decrease the increment of the slide\&. Default value: 3
+.RE
+.SS "Output section"
+.PP
+\fB\-plot\fR \fItoggle\fR
+.RS 4
+On selection a graph of the sequence (X axis) plotted against the coding score (Y axis) will be displayed\&. Sequence above the green line is coding, that below the red line is non\-coding\&. Default value: N
+.RE
+.PP
+\fB\-outfile\fR \fIreport\fR
+.RS 4
+.RE
+.PP
+\fB\-graph\fR \fIxygraph\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+tcode is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/godef.1e
+++ emboss-6.4.0/debian/manpages/godef.1e
@@ -0,0 +1,87 @@
+'\" t
+.\"     Title: GODEF
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "GODEF" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+godef \- Find GO ontology terms by definition
+.SH "SYNOPSIS"
+.HP \w'\fBgodef\fR\ 'u
+\fBgodef\fR \fB\-query\ \fR\fB\fIstring\fR\fR [\fB\-namespace\ \fR\fB\fIlist\fR\fR] \fB\-subclasses\ \fR\fB\fIboolean\fR\fR \fB\-obsolete\ \fR\fB\fIboolean\fR\fR \fB\-godef\ \fR\fB\fIoutobo\fR\fR
+.HP \w'\fBgodef\fR\ 'u
+\fBgodef\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBgodef\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Ontology:GO,Data retrieval:Ontology data" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-query\fR \fIstring\fR
+.RS 4
+.RE
+.SS "Additional section"
+.PP
+\fB\-namespace\fR \fIlist\fR
+.RS 4
+By default all terms are returned\&. Searches can be limited to one or a few namespaces\&. Default value: *
+.RE
+.SS "Advanced section"
+.PP
+\fB\-subclasses\fR \fIboolean\fR
+.RS 4
+Extend the query matches to include all terms which are specialisations (GO sub\-classes) of the matched type\&. Default value: N
+.RE
+.PP
+\fB\-obsolete\fR \fIboolean\fR
+.RS 4
+The default behaviour is to not use or return obsolete terms\&. This option if set will include all terms\&. Default value: N
+.RE
+.SS "Output section"
+.PP
+\fB\-godef\fR \fIoutobo\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+godef is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/showpep.1e
+++ emboss-6.4.0/debian/manpages/showpep.1e
@@ -0,0 +1,178 @@
+'\" t
+.\"     Title: SHOWPEP
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "SHOWPEP" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+showpep \- Displays protein sequences with features in pretty format
+.SH "SYNOPSIS"
+.HP \w'\fBshowpep\fR\ 'u
+\fBshowpep\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-format\ \fR\fB\fIlist\fR\fR \fB\-things\ \fR\fB\fIlist\fR\fR [\fB\-uppercase\ \fR\fB\fIrange\fR\fR] [\fB\-highlight\ \fR\fB\fIrange\fR\fR] [\fB\-annotation\ \fR\fB\fIrange\fR\fR] [\fB\-sourcematch\ \fR\fB\fIstring\fR\fR] [\fB\-typematch\ \fR\fB\fIstring\fR\fR] [\fB\-minscore\ \fR\fB\fIfloat\fR\fR] [\fB\-maxscore\ \fR\fB\fIfloat\fR\fR] [\fB\-tagmatch\ \fR\fB\fIstring\fR\fR] [\fB\-valuematch\ \fR\fB\fIstring\fR\fR] [\fB\-stricttags\ \fR\fB\fIboolean\fR\fR] \fB\-threeletter\ \fR\fB\fIboolean\fR\fR \fB\-number\ \fR\fB\fIboolean\fR\fR \fB\-width\ \fR\fB\fIinteger\fR\fR \fB\-length\ \fR\fB\fIinteger\fR\fR \fB\-margin\ \fR\fB\fIinteger\fR\fR \fB\-name\ \fR\fB\fIboolean\fR\fR \fB\-description\ \fR\fB\fIboolean\fR\fR \fB\-offset\ \fR\fB\fIinteger\fR\fR \fB\-html\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBshowpep\fR\ 'u
+\fBshowpep\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBshowpep\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Display" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqall\fR
+.RS 4
+.RE
+.SS "Required section"
+.PP
+\fB\-format\fR \fIlist\fR
+.RS 4
+Default value: 2
+.RE
+.PP
+\fB\-things\fR \fIlist\fR
+.RS 4
+Specify a list of one or more code characters in the order in which you wish things to be displayed one above the other down the page\&. For example if you wish to see things displayed in the order: sequence, ticks line, blank line; then you should enter \*(AqS,T,B\*(Aq\&. Default value: B,N,T,S,A,F
+.RE
+.SS "Additional section"
+.PP
+\fB\-uppercase\fR \fIrange\fR
+.RS 4
+Regions to put in uppercase\&. If this is left blank, then the sequence case is left alone\&. A set of regions is specified by a set of pairs of positions\&. The positions are integers\&. They are separated by any non\-digit, non\-alpha character\&. Examples of region specifications are: 24\-45, 56\-78 1:45, 67=99;765\&.\&.888 1,5,8,10,23,45,57,99
+.RE
+.PP
+\fB\-highlight\fR \fIrange\fR
+.RS 4
+Regions to colour if formatting for HTML\&. If this is left blank, then the sequence is left alone\&. A set of regions is specified by a set of pairs of positions\&. The positions are integers\&. They are followed by any valid HTML font colour\&. Examples of region specifications are: 24\-45 blue 56\-78 orange 1\-100 green 120\-156 red A file of ranges to colour (one range per line) can be specified as \*(Aq@filename\*(Aq\&.
+.RE
+.PP
+\fB\-annotation\fR \fIrange\fR
+.RS 4
+Regions to annotate by marking\&. If this is left blank, then no annotation is added\&. A set of regions is specified by a set of pairs of positions followed by optional text\&. The positions are integers\&. They are followed by any text (but not digits when on the command\-line)\&. Examples of region specifications are: 24\-45 new domain 56\-78 match to Mouse 1\-100 First part 120\-156 oligo A file of ranges to annotate (one range per line) can be specified as \*(Aq@filename\*(Aq\&.
+.RE
+.SS "Feature display options"
+.PP
+\fB\-sourcematch\fR \fIstring\fR
+.RS 4
+By default any feature source in the feature table is shown\&. You can set this to match any feature source you wish to show\&. The source name is usually either the name of the program that detected the feature or it is the feature table (eg: EMBL) that the feature came from\&. The source may be wildcarded by using \*(Aq*\*(Aq\&. If you wish to show more than one source, separate their names with the character \*(Aq|\*(Aq, eg: gene* | embl Default value: *
+.RE
+.PP
+\fB\-typematch\fR \fIstring\fR
+.RS 4
+By default any feature type in the feature table is shown\&. You can set this to match any feature type you wish to show\&. See http://www\&.ebi\&.ac\&.uk/embl/WebFeat/ for a list of the EMBL feature types and see Appendix A of the Swissprot user manual in http://www\&.expasy\&.org/sprot/userman\&.html for a list of the Swissprot feature types\&. The type may be wildcarded by using \*(Aq*\*(Aq\&. If you wish to show more than one type, separate their names with the character \*(Aq|\*(Aq, eg: *UTR | intron Default value: *
+.RE
+.PP
+\fB\-minscore\fR \fIfloat\fR
+.RS 4
+Minimum score of feature to display (see also maxscore) Default value: 0\&.0
+.RE
+.PP
+\fB\-maxscore\fR \fIfloat\fR
+.RS 4
+Maximum score of feature to display\&. If both minscore and maxscore are zero (the default), then any score is ignored Default value: 0\&.0
+.RE
+.PP
+\fB\-tagmatch\fR \fIstring\fR
+.RS 4
+Tags are the types of extra values that a feature may have\&. By default any feature tag in the feature table is shown\&. You can set this to match any feature tag you wish to show\&. The tag may be wildcarded by using \*(Aq*\*(Aq\&. If you wish to show more than one tag, separate their names with the character \*(Aq|\*(Aq, eg: gene | label Default value: *
+.RE
+.PP
+\fB\-valuematch\fR \fIstring\fR
+.RS 4
+Tag values are the values associated with a feature tag\&. Tags are the types of extra values that a feature may have\&. By default any feature tag value in the feature table is shown\&. You can set this to match any feature tag value you wish to show\&. The tag value may be wildcarded by using \*(Aq*\*(Aq\&. If you wish to show more than one tag value, separate their names with the character \*(Aq|\*(Aq, eg: pax* | 10 Default value: *
+.RE
+.PP
+\fB\-stricttags\fR \fIboolean\fR
+.RS 4
+By default if any tag/value pair in a feature matches the specified tag and value, then all the tags/value pairs of that feature will be displayed\&. If this is set to be true, then only those tag/value pairs in a feature that match the specified tag and value will be displayed\&. Default value: N
+.RE
+.SS "Advanced section"
+.PP
+\fB\-threeletter\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-number\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-width\fR \fIinteger\fR
+.RS 4
+Default value: 60
+.RE
+.PP
+\fB\-length\fR \fIinteger\fR
+.RS 4
+.RE
+.PP
+\fB\-margin\fR \fIinteger\fR
+.RS 4
+Default value: 10
+.RE
+.PP
+\fB\-name\fR \fIboolean\fR
+.RS 4
+Set this to be false if you do not wish to display the ID name of the sequence Default value: Y
+.RE
+.PP
+\fB\-description\fR \fIboolean\fR
+.RS 4
+Set this to be false if you do not wish to display the description of the sequence Default value: Y
+.RE
+.PP
+\fB\-offset\fR \fIinteger\fR
+.RS 4
+Default value: 1
+.RE
+.PP
+\fB\-html\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+showpep is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/wossoutput.1e
+++ emboss-6.4.0/debian/manpages/wossoutput.1e
@@ -0,0 +1,139 @@
+'\" t
+.\"     Title: WOSSOUTPUT
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "WOSSOUTPUT" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+wossoutput \- Finds programs by EDAM output data
+.SH "SYNOPSIS"
+.HP \w'\fBwossoutput\fR\ 'u
+\fBwossoutput\fR \fB\-identifier\ \fR\fB\fIstring\fR\fR [\fB\-explode\ \fR\fB\fIboolean\fR\fR] [\fB\-showkeywords\ \fR\fB\fIboolean\fR\fR] \fB\-sensitive\ \fR\fB\fIboolean\fR\fR \fB\-subclasses\ \fR\fB\fIboolean\fR\fR \fB\-obsolete\ \fR\fB\fIboolean\fR\fR \fB\-emboss\ \fR\fB\fIboolean\fR\fR \fB\-embassy\ \fR\fB\fIboolean\fR\fR \fB\-showembassy\ \fR\fB\fIstring\fR\fR \fB\-colon\ \fR\fB\fIboolean\fR\fR \fB\-gui\ \fR\fB\fIboolean\fR\fR [\fB\-outfile\ \fR\fB\fIoutfile\fR\fR] [\fB\-html\ \fR\fB\fItoggle\fR\fR] [\fB\-groups\ \fR\fB\fIboolean\fR\fR] [\fB\-alphabetic\ \fR\fB\fIboolean\fR\fR]
+.HP \w'\fBwossoutput\fR\ 'u
+\fBwossoutput\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBwossoutput\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Ontology:EDAM,Documentation" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-identifier\fR \fIstring\fR
+.RS 4
+.RE
+.SS "Additional section"
+.PP
+\fB\-explode\fR \fIboolean\fR
+.RS 4
+The groups that EMBOSS applications belong to have two forms, exploded and not exploded\&. The exploded group names are more numerous and often vaguely phrased than the non\-exploded ones\&. The exploded names are formed from definitions of the group names that start like NAME1:NAME2 and which are then expanded into many combinations of the names as: \*(AqNAME1\*(Aq, \*(AqNAME2\*(Aq, \*(AqNAME1 NAME2\*(Aq, NAME2 NAME1\*(Aq\&. The non\-expanded names are simply like: \*(AqNAME1 NAME2\*(Aq\&. Default value: N
+.RE
+.PP
+\fB\-showkeywords\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.SS "Advanced section"
+.PP
+\fB\-sensitive\fR \fIboolean\fR
+.RS 4
+By default, the query keywords are matched against the EDAM term names (and synonyms) only\&. This option also matches the keywords against the EDAM term definitions and will therefore (typically) report more matches\&. Default value: N
+.RE
+.PP
+\fB\-subclasses\fR \fIboolean\fR
+.RS 4
+Extend the query matches to include all terms which are specialisations (EDAM sub\-classes) of the matched type\&. Default value: Y
+.RE
+.PP
+\fB\-obsolete\fR \fIboolean\fR
+.RS 4
+The default behaviour is to not use or return obsolete terms\&. This option if set will include all terms\&. Default value: N
+.RE
+.PP
+\fB\-emboss\fR \fIboolean\fR
+.RS 4
+If you use this option then EMBOSS program documentation will be searched\&. If this option is set to be false, then only the EMBASSY programs will be searched (if the \-embassy option is true)\&. EMBASSY programs are not strictly part of EMBOSS, but use the same code libraries and share the same look and feel, but are generally developed by people who wish the programs to be outside of the GNU Public Licence scheme Default value: Y
+.RE
+.PP
+\fB\-embassy\fR \fIboolean\fR
+.RS 4
+If you use this option then EMBASSY program documentation will be searched\&. If this option is set to be false, then only the EMBOSS programs will be searched (if the \-emboss option is true)\&. EMBASSY programs are not strictly part of EMBOSS, but use the same code libraries and share the same look and feel, but are generally developed by people who wish the programs to be outside of the GNU Public Licence scheme Default value: Y
+.RE
+.PP
+\fB\-showembassy\fR \fIstring\fR
+.RS 4
+If you use this option then this EMBASSY package program documentation will be searched\&. EMBASSY programs are not strictly part of EMBOSS, but use the same code libraries and share the same look and feel, but are generally developed by people who wish the programs to be outside of the GNU Public Licence scheme
+.RE
+.PP
+\fB\-colon\fR \fIboolean\fR
+.RS 4
+The groups that EMBOSS applications belong to up to two levels, for example the primary group \*(AqALIGNMENT\*(Aq has several sub\-groups, or second\-level groups, e\&.g\&.: CONSENSUS, DIFFERENCES, DOT PLOTS, GLOBAL, LOCAL, MULTIPLE\&. To aid programs that parse the output of wossname that require the names of these subgroups, a colon \*(Aq:\*(Aq will be placed between the first and second level of the group name if this option is true\&. Note: This does not apply if the group names have been exploded with the \*(Aqexplode\*(Aq option\&. Default value: N
+.RE
+.PP
+\fB\-gui\fR \fIboolean\fR
+.RS 4
+This option is intended to help those who are designing Graphical User Interfaces to the EMBOSS applications\&. Some EMBOSS programs are inappropriate for running in a GUI, these include other menu programs and interactive editors\&. This option allows you to only report those programs that can be run from a GUI Default value: N
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+Default value: stdout
+.RE
+.SS "Html section"
+.PP
+\fB\-html\fR \fItoggle\fR
+.RS 4
+If you are sending the output to a file, this will format it for displaying as a table in a WWW document\&. Default value: N
+.RE
+.PP
+\fB\-groups\fR \fIboolean\fR
+.RS 4
+If you use this option, then only the group names will be output to the file Default value: N
+.RE
+.PP
+\fB\-alphabetic\fR \fIboolean\fR
+.RS 4
+If you use this option, then you will get a single list of the program names and descriptions instead of the programs being listed in their functional groups\&. Default value: N
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+wossoutput is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/abiview.1e
+++ emboss-6.4.0/debian/manpages/abiview.1e
@@ -0,0 +1,108 @@
+'\" t
+.\"     Title: ABIVIEW
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "ABIVIEW" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+abiview \- Display the trace in an ABI sequencer file
+.SH "SYNOPSIS"
+.HP \w'\fBabiview\fR\ 'u
+\fBabiview\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR \fB\-outseq\ \fR\fB\fIseqout\fR\fR \fB\-graph\ \fR\fB\fIxygraph\fR\fR [\fB\-startbase\ \fR\fB\fIinteger\fR\fR] [\fB\-endbase\ \fR\fB\fIinteger\fR\fR] \fB\-separate\ \fR\fB\fIboolean\fR\fR [\fB\-yticks\ \fR\fB\fIboolean\fR\fR] [\fB\-sequence\ \fR\fB\fIboolean\fR\fR] [\fB\-window\ \fR\fB\fIinteger\fR\fR] [\fB\-bases\ \fR\fB\fIstring\fR\fR]
+.HP \w'\fBabiview\fR\ 'u
+\fBabiview\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBabiview\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Data retrieval:Sequence data,Display" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-infile\fR \fIinfile\fR
+.RS 4
+.RE
+.SS "Output section"
+.PP
+\fB\-outseq\fR \fIseqout\fR
+.RS 4
+.RE
+.PP
+\fB\-graph\fR \fIxygraph\fR
+.RS 4
+.RE
+.PP
+\fB\-startbase\fR \fIinteger\fR
+.RS 4
+.RE
+.PP
+\fB\-endbase\fR \fIinteger\fR
+.RS 4
+Last sequence base to report or display\&. If the default is set to zero then the value of this is taken as the maximum number of bases\&.
+.RE
+.PP
+\fB\-separate\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-yticks\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-sequence\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-window\fR \fIinteger\fR
+.RS 4
+Default value: 40
+.RE
+.PP
+\fB\-bases\fR \fIstring\fR
+.RS 4
+Default value: GATC
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+abiview is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/showalign.1e
+++ emboss-6.4.0/debian/manpages/showalign.1e
@@ -0,0 +1,163 @@
+'\" t
+.\"     Title: SHOWALIGN
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "SHOWALIGN" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+showalign \- Display a multiple sequence alignment in pretty format
+.SH "SYNOPSIS"
+.HP \w'\fBshowalign\fR\ 'u
+\fBshowalign\fR \fB\-sequence\ \fR\fB\fIseqset\fR\fR [\fB\-matrix\ \fR\fB\fImatrix\fR\fR] [\fB\-refseq\ \fR\fB\fIstring\fR\fR] [\fB\-bottom\ \fR\fB\fIboolean\fR\fR] [\fB\-show\ \fR\fB\fIlist\fR\fR] [\fB\-order\ \fR\fB\fIlist\fR\fR] [\fB\-similarcase\ \fR\fB\fIboolean\fR\fR] [\fB\-consensus\ \fR\fB\fIboolean\fR\fR] \fB\-uppercase\ \fR\fB\fIrange\fR\fR \fB\-number\ \fR\fB\fIboolean\fR\fR \fB\-ruler\ \fR\fB\fIboolean\fR\fR \fB\-width\ \fR\fB\fIinteger\fR\fR \fB\-margin\ \fR\fB\fIinteger\fR\fR \fB\-html\ \fR\fB\fIboolean\fR\fR \fB\-highlight\ \fR\fB\fIrange\fR\fR \fB\-plurality\ \fR\fB\fIfloat\fR\fR \fB\-setcase\ \fR\fB\fIfloat\fR\fR \fB\-identity\ \fR\fB\fIfloat\fR\fR \fB\-gaps\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBshowalign\fR\ 'u
+\fBshowalign\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBshowalign\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Alignment:Multiple,Data retrieval:Sequence data" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqset\fR
+.RS 4
+The sequence alignment to be displayed\&.
+.RE
+.PP
+\fB\-matrix\fR \fImatrix\fR
+.RS 4
+This is the scoring matrix file used when comparing sequences\&. By default it is the file \*(AqEBLOSUM62\*(Aq (for proteins) or the file \*(AqEDNAFULL\*(Aq (for nucleic sequences)\&. These files are found in the \*(Aqdata\*(Aq directory of the EMBOSS installation\&.
+.RE
+.SS "Additional section"
+.PP
+\fB\-refseq\fR \fIstring\fR
+.RS 4
+If you give the number in the alignment or the name of a sequence, it will be taken to be the reference sequence\&. The reference sequence is always shown in full and is the one against which all the other sequences are compared\&. If this is set to 0 then the consensus sequence will be used as the reference sequence\&. By default the consensus sequence is used as the reference sequence\&.
+.RE
+.PP
+\fB\-bottom\fR \fIboolean\fR
+.RS 4
+If this is true then the reference sequence is displayed at the bottom of the alignment instead of the top\&. Default value: Y
+.RE
+.PP
+\fB\-show\fR \fIlist\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-order\fR \fIlist\fR
+.RS 4
+Default value: I
+.RE
+.PP
+\fB\-similarcase\fR \fIboolean\fR
+.RS 4
+If this is set True, then when \-show is set to \*(AqSimilarities\*(Aq or \*(AqNon\-identities\*(Aq and a residue is similar but not identical to the reference sequence residue, it will be changed to lower\-case\&. If \-show is set to \*(AqAll\*(Aq then non\-identical, non\-similar residues will be changed to lower\-case\&. If this is False then no change to the case of the residues is made on the basis of their similarity to the reference sequence\&. Default value: Y
+.RE
+.PP
+\fB\-consensus\fR \fIboolean\fR
+.RS 4
+If this is true then the consensus line is displayed\&. Default value: Y
+.RE
+.SS "Advanced section"
+.PP
+\fB\-uppercase\fR \fIrange\fR
+.RS 4
+Regions to put in uppercase\&. If this is left blank, then the sequence case is left alone\&. A set of regions is specified by a set of pairs of positions\&. The positions are integers\&. They are separated by any non\-digit, non\-alpha character\&. Examples of region specifications are: 24\-45, 56\-78 1:45, 67=99;765\&.\&.888 1,5,8,10,23,45,57,99
+.RE
+.PP
+\fB\-number\fR \fIboolean\fR
+.RS 4
+If this option is true then a line giving the positions in the alignment is displayed every 10 characters above the alignment\&. Default value: Y
+.RE
+.PP
+\fB\-ruler\fR \fIboolean\fR
+.RS 4
+If this option is true then a ruler line marking every 5th and 10th character in the alignment is displayed\&. Default value: Y
+.RE
+.PP
+\fB\-width\fR \fIinteger\fR
+.RS 4
+Default value: 60
+.RE
+.PP
+\fB\-margin\fR \fIinteger\fR
+.RS 4
+This sets the length of the left\-hand margin for sequence names\&. If the margin is set at 0 then no margin and no names are displayed\&. If the margin is set to a value that is less than the length of a sequence name then the sequence name is displayed truncated to the length of the margin\&. If the margin is set to \-1 then the minimum margin width that will allow all the sequence names to be displayed in full plus a space at the end of the name will automatically be selected\&. Default value: \-1
+.RE
+.PP
+\fB\-html\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-highlight\fR \fIrange\fR
+.RS 4
+Regions to colour if formatting for HTML\&. If this is left blank, then the sequence is left alone\&. A set of regions is specified by a set of pairs of positions\&. The positions are integers\&. They are followed by any valid HTML font colour\&. Examples of region specifications are: 24\-45 blue 56\-78 orange 1\-100 green 120\-156 red A file of ranges to colour (one range per line) can be specified as \*(Aq@filename\*(Aq\&.
+.RE
+.PP
+\fB\-plurality\fR \fIfloat\fR
+.RS 4
+Set a cut\-off for the % of positive scoring matches below which there is no consensus\&. The default plurality is taken as 50% of the total weight of all the sequences in the alignment\&. Default value: 50\&.0
+.RE
+.PP
+\fB\-setcase\fR \fIfloat\fR
+.RS 4
+Sets the threshold for the scores of the positive matches above which the consensus is in upper\-case and below which the consensus is in lower\-case\&. By default this is set to be half of the (weight\-adjusted) number of sequences in the alignment\&. Default value: @( $(sequence\&.totweight) / 2)
+.RE
+.PP
+\fB\-identity\fR \fIfloat\fR
+.RS 4
+Provides the facility of setting the required number of identities at a position for it to give a consensus\&. Therefore, if this is set to 100% only columns of identities contribute to the consensus\&. Default value: 0\&.0
+.RE
+.PP
+\fB\-gaps\fR \fIboolean\fR
+.RS 4
+If this option is true then gap characters can appear in the consensus\&. The alternative is \*(AqN\*(Aq for nucleotide, or \*(AqX\*(Aq for protein Default value: Y
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+showalign is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/ontogetsibs.1e
+++ emboss-6.4.0/debian/manpages/ontogetsibs.1e
@@ -0,0 +1,77 @@
+'\" t
+.\"     Title: ONTOGETSIBS
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "ONTOGETSIBS" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+ontogetsibs \- Get ontology term(s) by id with common parent
+.SH "SYNOPSIS"
+.HP \w'\fBontogetsibs\fR\ 'u
+\fBontogetsibs\fR \fB\-oboterms\ \fR\fB\fIobo\fR\fR [\fB\-obsolete\ \fR\fB\fIboolean\fR\fR] \fB\-outfile\ \fR\fB\fIoutobo\fR\fR
+.HP \w'\fBontogetsibs\fR\ 'u
+\fBontogetsibs\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBontogetsibs\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Ontology,Data retrieval:Ontology data" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-oboterms\fR \fIobo\fR
+.RS 4
+.RE
+.SS "Additional section"
+.PP
+\fB\-obsolete\fR \fIboolean\fR
+.RS 4
+The default behaviour is to not use or return obsolete terms\&. This option if set will include all terms\&. Default value: N
+.RE
+.SS "Advanced section"
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutobo\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+ontogetsibs is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/descseq.1e
+++ emboss-6.4.0/debian/manpages/descseq.1e
@@ -0,0 +1,85 @@
+'\" t
+.\"     Title: DESCSEQ
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "DESCSEQ" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+descseq \- Alter the name or description of a sequence\&.
+.SH "SYNOPSIS"
+.HP \w'\fBdescseq\fR\ 'u
+\fBdescseq\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR [\fB\-name\ \fR\fB\fIstring\fR\fR] [\fB\-description\ \fR\fB\fIstring\fR\fR] \fB\-append\ \fR\fB\fIboolean\fR\fR \fB\-outseq\ \fR\fB\fIseqout\fR\fR
+.HP \w'\fBdescseq\fR\ 'u
+\fBdescseq\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBdescseq\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIsequence\fR
+.RS 4
+.RE
+.SS "Additional section"
+.PP
+\fB\-name\fR \fIstring\fR
+.RS 4
+.RE
+.PP
+\fB\-description\fR \fIstring\fR
+.RS 4
+.RE
+.SS "Advanced section"
+.PP
+\fB\-append\fR \fIboolean\fR
+.RS 4
+This allows you to append the name or description you have given on to the end of the existing name or description of the sequence\&. Default value: N
+.RE
+.SS "Output section"
+.PP
+\fB\-outseq\fR \fIseqout\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+descseq is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/isdbdata.1e
+++ emboss-6.4.0/debian/manpages/isdbdata.1e
@@ -0,0 +1,79 @@
+'\" t
+.\"     Title: ISDBDATA
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "ISDBDATA" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+isdbdata \- Check whether a supplied string is a known data type/identifier name
+.SH "SYNOPSIS"
+.HP \w'\fBisdbdata\fR\ 'u
+\fBisdbdata\fR [\fB\-term\ \fR\fB\fIstring\fR\fR] [\fB\-termout\ \fR\fB\fItoggle\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBisdbdata\fR\ 'u
+\fBisdbdata\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBisdbdata\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Information" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-term\fR \fIstring\fR
+.RS 4
+.RE
+.SS "Required section"
+.SS "Additional section"
+.PP
+\fB\-termout\fR \fItoggle\fR
+.RS 4
+This option will write to file the term statement from the EDAM ontology with a name that matches the supplied string\&. Only the EDAM \*(Aqdata\*(Aq branch (data type or identifier) is checked\&. Default value: N
+.RE
+.SS "Advanced section"
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+Default value: stdout
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+isdbdata is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/edamhasoutput.1e
+++ emboss-6.4.0/debian/manpages/edamhasoutput.1e
@@ -0,0 +1,92 @@
+'\" t
+.\"     Title: EDAMHASOUTPUT
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "EDAMHASOUTPUT" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+edamhasoutput \- Find EDAM ontology terms by has_output relation
+.SH "SYNOPSIS"
+.HP \w'\fBedamhasoutput\fR\ 'u
+\fBedamhasoutput\fR \fB\-identifier\ \fR\fB\fIstring\fR\fR [\fB\-namespace\ \fR\fB\fIlist\fR\fR] \fB\-sensitive\ \fR\fB\fIboolean\fR\fR \fB\-subclasses\ \fR\fB\fIboolean\fR\fR \fB\-obsolete\ \fR\fB\fIboolean\fR\fR \fB\-edamhasoutput\ \fR\fB\fIoutobo\fR\fR
+.HP \w'\fBedamhasoutput\fR\ 'u
+\fBedamhasoutput\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBedamhasoutput\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Ontology:EDAM,Data retrieval:Ontology data" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-identifier\fR \fIstring\fR
+.RS 4
+.RE
+.SS "Additional section"
+.PP
+\fB\-namespace\fR \fIlist\fR
+.RS 4
+By default all terms are returned\&. Searches can be limited to one or a few namespaces\&. Default value: *
+.RE
+.SS "Advanced section"
+.PP
+\fB\-sensitive\fR \fIboolean\fR
+.RS 4
+By default, the query keywords are matched against the EDAM term names (and synonyms) only\&. This option also matches the keywords against the EDAM term definitions and will therefore (typically) report more matches\&. Default value: N
+.RE
+.PP
+\fB\-subclasses\fR \fIboolean\fR
+.RS 4
+Extend the query matches to include all terms which are specialisations (EDAM sub\-classes) of the matched type\&. Default value: N
+.RE
+.PP
+\fB\-obsolete\fR \fIboolean\fR
+.RS 4
+The default behaviour is to not use or return obsolete terms\&. This option if set will include all terms\&. Default value: N
+.RE
+.SS "Output section"
+.PP
+\fB\-edamhasoutput\fR \fIoutobo\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+edamhasoutput is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/edamhasinput.1e
+++ emboss-6.4.0/debian/manpages/edamhasinput.1e
@@ -0,0 +1,92 @@
+'\" t
+.\"     Title: EDAMHASINPUT
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "EDAMHASINPUT" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+edamhasinput \- Find EDAM ontology terms by has_input relation
+.SH "SYNOPSIS"
+.HP \w'\fBedamhasinput\fR\ 'u
+\fBedamhasinput\fR \fB\-identifier\ \fR\fB\fIstring\fR\fR [\fB\-namespace\ \fR\fB\fIlist\fR\fR] \fB\-sensitive\ \fR\fB\fIboolean\fR\fR \fB\-subclasses\ \fR\fB\fIboolean\fR\fR \fB\-obsolete\ \fR\fB\fIboolean\fR\fR \fB\-edamhasinput\ \fR\fB\fIoutobo\fR\fR
+.HP \w'\fBedamhasinput\fR\ 'u
+\fBedamhasinput\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBedamhasinput\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Ontology:EDAM,Data retrieval:Ontology data" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-identifier\fR \fIstring\fR
+.RS 4
+.RE
+.SS "Additional section"
+.PP
+\fB\-namespace\fR \fIlist\fR
+.RS 4
+By default all terms are returned\&. Searches can be limited to one or a few namespaces\&. Default value: *
+.RE
+.SS "Advanced section"
+.PP
+\fB\-sensitive\fR \fIboolean\fR
+.RS 4
+By default, the query keywords are matched against the EDAM term names (and synonyms) only\&. This option also matches the keywords against the EDAM term definitions and will therefore (typically) report more matches\&. Default value: N
+.RE
+.PP
+\fB\-subclasses\fR \fIboolean\fR
+.RS 4
+Extend the query matches to include all terms which are specialisations (EDAM sub\-classes) of the matched type\&. Default value: N
+.RE
+.PP
+\fB\-obsolete\fR \fIboolean\fR
+.RS 4
+The default behaviour is to not use or return obsolete terms\&. This option if set will include all terms\&. Default value: N
+.RE
+.SS "Output section"
+.PP
+\fB\-edamhasinput\fR \fIoutobo\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+edamhasinput is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/seqtax.1e
+++ emboss-6.4.0/debian/manpages/seqtax.1e
@@ -0,0 +1,80 @@
+'\" t
+.\"     Title: SEQTAX
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "SEQTAX" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+seqtax \- Extract a list of taxonomy ids from a sequence entry
+.SH "SYNOPSIS"
+.HP \w'\fBseqtax\fR\ 'u
+\fBseqtax\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-html\ \fR\fB\fIboolean\fR\fR]
+.HP \w'\fBseqtax\fR\ 'u
+\fBseqtax\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBseqtax\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Ontology:Taxonomy" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIsequence\fR
+.RS 4
+.RE
+.SS "Required section"
+.SS "Additional section"
+.SS "Advanced section"
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+This is the file of NCBI taxonomy IDs that were found in the input sequnce entry\&.
+.RE
+.SS "Html section"
+.PP
+\fB\-html\fR \fIboolean\fR
+.RS 4
+If you are sending the output to a file, this will format it for displaying as a table in a WWW document\&. Default value: N
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+seqtax is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/helixturnhelix.1e
+++ emboss-6.4.0/debian/manpages/helixturnhelix.1e
@@ -0,0 +1,90 @@
+'\" t
+.\"     Title: HELIXTURNHELIX
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "HELIXTURNHELIX" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+helixturnhelix \- Identify nucleic acid\-binding motifs in protein sequences
+.SH "SYNOPSIS"
+.HP \w'\fBhelixturnhelix\fR\ 'u
+\fBhelixturnhelix\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR [\fB\-mean\ \fR\fB\fIfloat\fR\fR] [\fB\-sd\ \fR\fB\fIfloat\fR\fR] [\fB\-minsd\ \fR\fB\fIfloat\fR\fR] [\fB\-eightyseven\ \fR\fB\fIboolean\fR\fR] \fB\-outfile\ \fR\fB\fIreport\fR\fR
+.HP \w'\fBhelixturnhelix\fR\ 'u
+\fBhelixturnhelix\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBhelixturnhelix\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Protein:2D Structure,Protein:Domains" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqall\fR
+.RS 4
+.RE
+.SS "Additional section"
+.PP
+\fB\-mean\fR \fIfloat\fR
+.RS 4
+Default value: 238\&.71
+.RE
+.PP
+\fB\-sd\fR \fIfloat\fR
+.RS 4
+Default value: 293\&.61
+.RE
+.PP
+\fB\-minsd\fR \fIfloat\fR
+.RS 4
+Default value: 2\&.5
+.RE
+.PP
+\fB\-eightyseven\fR \fIboolean\fR
+.RS 4
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIreport\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+helixturnhelix is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/dbtell.1e
+++ emboss-6.4.0/debian/manpages/dbtell.1e
@@ -0,0 +1,79 @@
+'\" t
+.\"     Title: DBTELL
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "DBTELL" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+dbtell \- Display information about a public database
+.SH "SYNOPSIS"
+.HP \w'\fBdbtell\fR\ 'u
+\fBdbtell\fR \fB\-database\ \fR\fB\fIstring\fR\fR [\fB\-full\ \fR\fB\fIboolean\fR\fR] [\fB\-outfile\ \fR\fB\fIoutfile\fR\fR]
+.HP \w'\fBdbtell\fR\ 'u
+\fBdbtell\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBdbtell\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Data resources" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-database\fR \fIstring\fR
+.RS 4
+The name of the database defined locally for use by EMBOSS\&.
+.RE
+.SS "Additional section"
+.PP
+\fB\-full\fR \fIboolean\fR
+.RS 4
+The default behaviour is to report for relevant databases only basic information from the EMBOSS database definition Default value: N
+.RE
+.SS "Advanced section"
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+Default value: stdout
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+dbtell is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/seqgo.1e
+++ emboss-6.4.0/debian/manpages/seqgo.1e
@@ -0,0 +1,80 @@
+'\" t
+.\"     Title: SEQGO
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "SEQGO" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+seqgo \- Extract a list of GO terms from a sequence entry
+.SH "SYNOPSIS"
+.HP \w'\fBseqgo\fR\ 'u
+\fBseqgo\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-html\ \fR\fB\fIboolean\fR\fR]
+.HP \w'\fBseqgo\fR\ 'u
+\fBseqgo\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBseqgo\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Ontology:GO" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIsequence\fR
+.RS 4
+.RE
+.SS "Required section"
+.SS "Additional section"
+.SS "Advanced section"
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+This is the file of GO ontology terms that were found in the input sequnce entry\&.
+.RE
+.SS "Html section"
+.PP
+\fB\-html\fR \fIboolean\fR
+.RS 4
+If you are sending the output to a file, this will format it for displaying as a table in a WWW document\&. Default value: N
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+seqgo is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/isochore.1e
+++ emboss-6.4.0/debian/manpages/isochore.1e
@@ -0,0 +1,85 @@
+'\" t
+.\"     Title: ISOCHORE
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "ISOCHORE" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+isochore \- Plots isochores in DNA sequences
+.SH "SYNOPSIS"
+.HP \w'\fBisochore\fR\ 'u
+\fBisochore\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR [\fB\-window\ \fR\fB\fIinteger\fR\fR] [\fB\-shift\ \fR\fB\fIinteger\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR \fB\-graph\ \fR\fB\fIxygraph\fR\fR
+.HP \w'\fBisochore\fR\ 'u
+\fBisochore\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBisochore\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Composition" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIsequence\fR
+.RS 4
+.RE
+.SS "Additional section"
+.PP
+\fB\-window\fR \fIinteger\fR
+.RS 4
+Default value: 1000
+.RE
+.PP
+\fB\-shift\fR \fIinteger\fR
+.RS 4
+Default value: 100
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.PP
+\fB\-graph\fR \fIxygraph\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+isochore is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/wosstopic.1e
+++ emboss-6.4.0/debian/manpages/wosstopic.1e
@@ -0,0 +1,139 @@
+'\" t
+.\"     Title: WOSSTOPIC
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "WOSSTOPIC" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+wosstopic \- Finds programs by EDAM topic
+.SH "SYNOPSIS"
+.HP \w'\fBwosstopic\fR\ 'u
+\fBwosstopic\fR \fB\-identifier\ \fR\fB\fIstring\fR\fR [\fB\-explode\ \fR\fB\fIboolean\fR\fR] [\fB\-showkeywords\ \fR\fB\fIboolean\fR\fR] \fB\-sensitive\ \fR\fB\fIboolean\fR\fR \fB\-subclasses\ \fR\fB\fIboolean\fR\fR \fB\-obsolete\ \fR\fB\fIboolean\fR\fR \fB\-emboss\ \fR\fB\fIboolean\fR\fR \fB\-embassy\ \fR\fB\fIboolean\fR\fR \fB\-showembassy\ \fR\fB\fIstring\fR\fR \fB\-colon\ \fR\fB\fIboolean\fR\fR \fB\-gui\ \fR\fB\fIboolean\fR\fR [\fB\-outfile\ \fR\fB\fIoutfile\fR\fR] [\fB\-html\ \fR\fB\fItoggle\fR\fR] [\fB\-groups\ \fR\fB\fIboolean\fR\fR] [\fB\-alphabetic\ \fR\fB\fIboolean\fR\fR]
+.HP \w'\fBwosstopic\fR\ 'u
+\fBwosstopic\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBwosstopic\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Ontology:EDAM,Documentation" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-identifier\fR \fIstring\fR
+.RS 4
+.RE
+.SS "Additional section"
+.PP
+\fB\-explode\fR \fIboolean\fR
+.RS 4
+The groups that EMBOSS applications belong to have two forms, exploded and not exploded\&. The exploded group names are more numerous and often vaguely phrased than the non\-exploded ones\&. The exploded names are formed from definitions of the group names that start like NAME1:NAME2 and which are then expanded into many combinations of the names as: \*(AqNAME1\*(Aq, \*(AqNAME2\*(Aq, \*(AqNAME1 NAME2\*(Aq, NAME2 NAME1\*(Aq\&. The non\-expanded names are simply like: \*(AqNAME1 NAME2\*(Aq\&. Default value: N
+.RE
+.PP
+\fB\-showkeywords\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.SS "Advanced section"
+.PP
+\fB\-sensitive\fR \fIboolean\fR
+.RS 4
+By default, the query keywords are matched against the EDAM term names (and synonyms) only\&. This option also matches the keywords against the EDAM term definitions and will therefore (typically) report more matches\&. Default value: N
+.RE
+.PP
+\fB\-subclasses\fR \fIboolean\fR
+.RS 4
+Extend the query matches to include all terms which are specialisations (EDAM sub\-classes) of the matched type\&. Default value: Y
+.RE
+.PP
+\fB\-obsolete\fR \fIboolean\fR
+.RS 4
+The default behaviour is to not use or return obsolete terms\&. This option if set will include all terms\&. Default value: N
+.RE
+.PP
+\fB\-emboss\fR \fIboolean\fR
+.RS 4
+If you use this option then EMBOSS program documentation will be searched\&. If this option is set to be false, then only the EMBASSY programs will be searched (if the \-embassy option is true)\&. EMBASSY programs are not strictly part of EMBOSS, but use the same code libraries and share the same look and feel, but are generally developed by people who wish the programs to be outside of the GNU Public Licence scheme Default value: Y
+.RE
+.PP
+\fB\-embassy\fR \fIboolean\fR
+.RS 4
+If you use this option then EMBASSY program documentation will be searched\&. If this option is set to be false, then only the EMBOSS programs will be searched (if the \-emboss option is true)\&. EMBASSY programs are not strictly part of EMBOSS, but use the same code libraries and share the same look and feel, but are generally developed by people who wish the programs to be outside of the GNU Public Licence scheme Default value: Y
+.RE
+.PP
+\fB\-showembassy\fR \fIstring\fR
+.RS 4
+If you use this option then this EMBASSY package program documentation will be searched\&. EMBASSY programs are not strictly part of EMBOSS, but use the same code libraries and share the same look and feel, but are generally developed by people who wish the programs to be outside of the GNU Public Licence scheme
+.RE
+.PP
+\fB\-colon\fR \fIboolean\fR
+.RS 4
+The groups that EMBOSS applications belong to up to two levels, for example the primary group \*(AqALIGNMENT\*(Aq has several sub\-groups, or second\-level groups, e\&.g\&.: CONSENSUS, DIFFERENCES, DOT PLOTS, GLOBAL, LOCAL, MULTIPLE\&. To aid programs that parse the output of wossname that require the names of these subgroups, a colon \*(Aq:\*(Aq will be placed between the first and second level of the group name if this option is true\&. Note: This does not apply if the group names have been exploded with the \*(Aqexplode\*(Aq option\&. Default value: N
+.RE
+.PP
+\fB\-gui\fR \fIboolean\fR
+.RS 4
+This option is intended to help those who are designing Graphical User Interfaces to the EMBOSS applications\&. Some EMBOSS programs are inappropriate for running in a GUI, these include other menu programs and interactive editors\&. This option allows you to only report those programs that can be run from a GUI Default value: N
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+Default value: stdout
+.RE
+.SS "Html section"
+.PP
+\fB\-html\fR \fItoggle\fR
+.RS 4
+If you are sending the output to a file, this will format it for displaying as a table in a WWW document\&. Default value: N
+.RE
+.PP
+\fB\-groups\fR \fIboolean\fR
+.RS 4
+If you use this option, then only the group names will be output to the file Default value: N
+.RE
+.PP
+\fB\-alphabetic\fR \fIboolean\fR
+.RS 4
+If you use this option, then you will get a single list of the program names and descriptions instead of the programs being listed in their functional groups\&. Default value: N
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+wosstopic is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/etandem.1e
+++ emboss-6.4.0/debian/manpages/etandem.1e
@@ -0,0 +1,99 @@
+'\" t
+.\"     Title: ETANDEM
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "ETANDEM" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+etandem \- Finds tandem repeats in a nucleotide sequence
+.SH "SYNOPSIS"
+.HP \w'\fBetandem\fR\ 'u
+\fBetandem\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR \fB\-minrepeat\ \fR\fB\fIinteger\fR\fR \fB\-maxrepeat\ \fR\fB\fIinteger\fR\fR \fB\-threshold\ \fR\fB\fIinteger\fR\fR \fB\-mismatch\ \fR\fB\fIboolean\fR\fR \fB\-uniform\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIreport\fR\fR \fB\-origfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBetandem\fR\ 'u
+\fBetandem\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBetandem\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Repeats" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIsequence\fR
+.RS 4
+.RE
+.SS "Required section"
+.PP
+\fB\-minrepeat\fR \fIinteger\fR
+.RS 4
+Default value: 10
+.RE
+.PP
+\fB\-maxrepeat\fR \fIinteger\fR
+.RS 4
+Default value: $(minrepeat)
+.RE
+.SS "Advanced section"
+.PP
+\fB\-threshold\fR \fIinteger\fR
+.RS 4
+Default value: 20
+.RE
+.PP
+\fB\-mismatch\fR \fIboolean\fR
+.RS 4
+.RE
+.PP
+\fB\-uniform\fR \fIboolean\fR
+.RS 4
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIreport\fR
+.RS 4
+.RE
+.PP
+\fB\-origfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+etandem is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/printsextract.1e
+++ emboss-6.4.0/debian/manpages/printsextract.1e
@@ -0,0 +1,65 @@
+'\" t
+.\"     Title: PRINTSEXTRACT
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "PRINTSEXTRACT" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+printsextract \- Extract data from PRINTS database for use by pscan
+.SH "SYNOPSIS"
+.HP \w'\fBprintsextract\fR\ 'u
+\fBprintsextract\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR
+.HP \w'\fBprintsextract\fR\ 'u
+\fBprintsextract\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBprintsextract\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Database creation" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-infile\fR \fIinfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+printsextract is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/idtell.1e
+++ emboss-6.4.0/debian/manpages/idtell.1e
@@ -0,0 +1,74 @@
+'\" t
+.\"     Title: IDTELL
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "IDTELL" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+idtell \- Identify the type of a data identifier or query term
+.SH "SYNOPSIS"
+.HP \w'\fBidtell\fR\ 'u
+\fBidtell\fR [\fB\-identifier\ \fR\fB\fIstring\fR\fR] \fB\-dbref\ \fR\fB\fIdatafile\fR\fR
+.HP \w'\fBidtell\fR\ 'u
+\fBidtell\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBidtell\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Information" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-identifier\fR \fIstring\fR
+.RS 4
+.RE
+.PP
+\fB\-dbref\fR \fIdatafile\fR
+.RS 4
+File of database information including identifier, description, type, URL etc\&. Default value: dbref\&.dat
+.RE
+.SS "Required section"
+.SS "Additional section"
+.SS "Advanced section"
+.SS "Output section"
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+idtell is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/octanol.1e
+++ emboss-6.4.0/debian/manpages/octanol.1e
@@ -0,0 +1,96 @@
+'\" t
+.\"     Title: OCTANOL
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "OCTANOL" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+octanol \- Draw a White\-Wimley protein hydropathy plot
+.SH "SYNOPSIS"
+.HP \w'\fBoctanol\fR\ 'u
+\fBoctanol\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR [\fB\-datafile\ \fR\fB\fIdatafile\fR\fR] [\fB\-width\ \fR\fB\fIinteger\fR\fR] \fB\-graph\ \fR\fB\fIxygraph\fR\fR [\fB\-plotoctanol\ \fR\fB\fIboolean\fR\fR] [\fB\-plotinterface\ \fR\fB\fIboolean\fR\fR] [\fB\-plotdifference\ \fR\fB\fIboolean\fR\fR]
+.HP \w'\fBoctanol\fR\ 'u
+\fBoctanol\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBoctanol\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Protein:Properties" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIsequence\fR
+.RS 4
+.RE
+.PP
+\fB\-datafile\fR \fIdatafile\fR
+.RS 4
+Default value: Ewhite\-wimley\&.dat
+.RE
+.SS "Additional section"
+.PP
+\fB\-width\fR \fIinteger\fR
+.RS 4
+Default value: 19
+.RE
+.SS "Output section"
+.PP
+\fB\-graph\fR \fIxygraph\fR
+.RS 4
+.RE
+.PP
+\fB\-plotoctanol\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-plotinterface\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-plotdifference\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+octanol is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/infobase.1e
+++ emboss-6.4.0/debian/manpages/infobase.1e
@@ -0,0 +1,74 @@
+'\" t
+.\"     Title: INFOBASE
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "INFOBASE" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+infobase \- Return information on a given nucleotide base
+.SH "SYNOPSIS"
+.HP \w'\fBinfobase\fR\ 'u
+\fBinfobase\fR \fB\-code\ \fR\fB\fIstring\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBinfobase\fR\ 'u
+\fBinfobase\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBinfobase\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Data retrieval:Chemistry data" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-code\fR \fIstring\fR
+.RS 4
+Enter IUPAC nucleotide base codes, e\&.g\&. A, C, G, T, R, Y etc\&. Default value: ABCDGHKMNRSTUVWXY
+.RE
+.SS "Required section"
+.SS "Additional section"
+.SS "Advanced section"
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+infobase is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/cpgplot.1e
+++ emboss-6.4.0/debian/manpages/cpgplot.1e
@@ -0,0 +1,121 @@
+'\" t
+.\"     Title: CPGPLOT
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "CPGPLOT" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+cpgplot \- Identify and plot CpG islands in nucleotide sequence(s)
+.SH "SYNOPSIS"
+.HP \w'\fBcpgplot\fR\ 'u
+\fBcpgplot\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-window\ \fR\fB\fIinteger\fR\fR \fB\-minlen\ \fR\fB\fIinteger\fR\fR \fB\-minoe\ \fR\fB\fIfloat\fR\fR \fB\-minpc\ \fR\fB\fIfloat\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR \fB\-plot\ \fR\fB\fItoggle\fR\fR \fB\-graph\ \fR\fB\fIxygraph\fR\fR \fB\-obsexp\ \fR\fB\fIboolean\fR\fR \fB\-cg\ \fR\fB\fIboolean\fR\fR \fB\-pc\ \fR\fB\fIboolean\fR\fR \fB\-outfeat\ \fR\fB\fIfeatout\fR\fR
+.HP \w'\fBcpgplot\fR\ 'u
+\fBcpgplot\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBcpgplot\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:CpG Islands" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqall\fR
+.RS 4
+.RE
+.SS "Required section"
+.PP
+\fB\-window\fR \fIinteger\fR
+.RS 4
+The percentage CG content and the Observed frequency of CG is calculated within a window whose size is set by this parameter\&. The window is moved down the sequence and these statistics are calculated at each position that the window is moved to\&. Default value: 100
+.RE
+.PP
+\fB\-minlen\fR \fIinteger\fR
+.RS 4
+This sets the minimum length that a CpG island has to be before it is reported\&. Default value: 200
+.RE
+.PP
+\fB\-minoe\fR \fIfloat\fR
+.RS 4
+This sets the minimum average observed to expected ratio of C plus G to CpG in a set of 10 windows that are required before a CpG island is reported\&. Default value: 0\&.6
+.RE
+.PP
+\fB\-minpc\fR \fIfloat\fR
+.RS 4
+This sets the minimum average percentage of G plus C a set of 10 windows that are required before a CpG island is reported\&. Default value: 50\&.
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+This sets the name of the file holding the report of the input sequence name, CpG island parameters and the output details of any CpG islands that are found\&.
+.RE
+.PP
+\fB\-plot\fR \fItoggle\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-graph\fR \fIxygraph\fR
+.RS 4
+.RE
+.PP
+\fB\-obsexp\fR \fIboolean\fR
+.RS 4
+If this is set to true then the graph of the observed to expected ratio of C plus G to CpG within a window is displayed\&. Default value: Y
+.RE
+.PP
+\fB\-cg\fR \fIboolean\fR
+.RS 4
+If this is set to true then the graph of the regions which have been determined to be CpG islands is displayed\&. Default value: Y
+.RE
+.PP
+\fB\-pc\fR \fIboolean\fR
+.RS 4
+If this is set to true then the graph of the percentage C plus G within a window is displayed\&. Default value: Y
+.RE
+.PP
+\fB\-outfeat\fR \fIfeatout\fR
+.RS 4
+File for output features
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+cpgplot is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/ontogetobsolete.1e
+++ emboss-6.4.0/debian/manpages/ontogetobsolete.1e
@@ -0,0 +1,77 @@
+'\" t
+.\"     Title: ONTOGETOBSOLETE
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "ONTOGETOBSOLETE" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+ontogetobsolete \- Get ontology ontology terms
+.SH "SYNOPSIS"
+.HP \w'\fBontogetobsolete\fR\ 'u
+\fBontogetobsolete\fR \fB\-oboterms\ \fR\fB\fIobo\fR\fR [\fB\-subclasses\ \fR\fB\fIboolean\fR\fR] \fB\-outfile\ \fR\fB\fIoutobo\fR\fR
+.HP \w'\fBontogetobsolete\fR\ 'u
+\fBontogetobsolete\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBontogetobsolete\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Ontology,Data retrieval:Ontology data" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-oboterms\fR \fIobo\fR
+.RS 4
+.RE
+.SS "Additional section"
+.PP
+\fB\-subclasses\fR \fIboolean\fR
+.RS 4
+Extend the query matches to include all terms which are specialisations (sub\-classes) of the matched terms\&. Default value: N
+.RE
+.SS "Advanced section"
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutobo\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+ontogetobsolete is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/dbxedam.1e
+++ emboss-6.4.0/debian/manpages/dbxedam.1e
@@ -0,0 +1,122 @@
+'\" t
+.\"     Title: DBXEDAM
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "DBXEDAM" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+dbxedam \- Index the EDAM ontology using b+tree indices
+.SH "SYNOPSIS"
+.HP \w'\fBdbxedam\fR\ 'u
+\fBdbxedam\fR \fB\-dbname\ \fR\fB\fIstring\fR\fR \fB\-standardname\ \fR\fB\fIstring\fR\fR \fB\-dbresource\ \fR\fB\fIstring\fR\fR \fB\-directory\ \fR\fB\fIdirectory\fR\fR \fB\-filenames\ \fR\fB\fIstring\fR\fR \fB\-fields\ \fR\fB\fIlist\fR\fR \fB\-compressed\ \fR\fB\fIboolean\fR\fR \fB\-release\ \fR\fB\fIstring\fR\fR \fB\-date\ \fR\fB\fIstring\fR\fR \fB\-exclude\ \fR\fB\fIstring\fR\fR \fB\-indexoutdir\ \fR\fB\fIoutdir\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBdbxedam\fR\ 'u
+\fBdbxedam\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBdbxedam\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Database indexing" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-dbname\fR \fIstring\fR
+.RS 4
+Default value: edam
+.RE
+.PP
+\fB\-standardname\fR \fIstring\fR
+.RS 4
+Default value: $(dbname)
+.RE
+.PP
+\fB\-dbresource\fR \fIstring\fR
+.RS 4
+Default value: edamresource
+.RE
+.PP
+\fB\-directory\fR \fIdirectory\fR
+.RS 4
+Default value: \&.
+.RE
+.PP
+\fB\-filenames\fR \fIstring\fR
+.RS 4
+Default value: EDAM*\&.obo
+.RE
+.SS "Required section"
+.PP
+\fB\-fields\fR \fIlist\fR
+.RS 4
+Default value: *
+.RE
+.PP
+\fB\-compressed\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.SS "Advanced section"
+.PP
+\fB\-release\fR \fIstring\fR
+.RS 4
+Default value: 0\&.0
+.RE
+.PP
+\fB\-date\fR \fIstring\fR
+.RS 4
+Default value: 00/00/00
+.RE
+.PP
+\fB\-exclude\fR \fIstring\fR
+.RS 4
+.RE
+.SS "Output section"
+.PP
+\fB\-indexoutdir\fR \fIoutdir\fR
+.RS 4
+Default value: \&.
+.RE
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+dbxedam is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/ontogetup.1e
+++ emboss-6.4.0/debian/manpages/ontogetup.1e
@@ -0,0 +1,77 @@
+'\" t
+.\"     Title: ONTOGETUP
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "ONTOGETUP" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+ontogetup \- Get ontology term(s) by id of child
+.SH "SYNOPSIS"
+.HP \w'\fBontogetup\fR\ 'u
+\fBontogetup\fR \fB\-oboterms\ \fR\fB\fIobo\fR\fR [\fB\-obsolete\ \fR\fB\fIboolean\fR\fR] \fB\-outfile\ \fR\fB\fIoutobo\fR\fR
+.HP \w'\fBontogetup\fR\ 'u
+\fBontogetup\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBontogetup\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Ontology,Data retrieval:Ontology data" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-oboterms\fR \fIobo\fR
+.RS 4
+.RE
+.SS "Additional section"
+.PP
+\fB\-obsolete\fR \fIboolean\fR
+.RS 4
+The default behaviour is to not use or return obsolete terms\&. This option if set will include all terms\&. Default value: N
+.RE
+.SS "Advanced section"
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutobo\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+ontogetup is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/intconv.1e
+++ emboss-6.4.0/debian/manpages/intconv.1e
@@ -0,0 +1,70 @@
+'\" t
+.\"     Title: INTCONV
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "INTCONV" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+intconv \- Convert ints to ajints and longs to ajlongs
+.SH "SYNOPSIS"
+.HP \w'\fBintconv\fR\ 'u
+\fBintconv\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBintconv\fR\ 'u
+\fBintconv\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBintconv\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Test" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-infile\fR \fIinfile\fR
+.RS 4
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+intconv is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/entrailsbook.1e
+++ emboss-6.4.0/debian/manpages/entrailsbook.1e
@@ -0,0 +1,71 @@
+'\" t
+.\"     Title: ENTRAILSBOOK
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "ENTRAILSBOOK" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+entrailsbook \- Reports the internal structures in EMBOSS book format
+.SH "SYNOPSIS"
+.HP \w'\fBentrailsbook\fR\ 'u
+\fBentrailsbook\fR \fB\-tables\ \fR\fB\fIlist\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBentrailsbook\fR\ 'u
+\fBentrailsbook\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBentrailsbook\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Misc" command group(s)\&.
+.SH "OPTIONS"
+.SS "required section"
+.PP
+\fB\-tables\fR \fIlist\fR
+.RS 4
+Default value: all
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+entrailsbook is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/water.1e
+++ emboss-6.4.0/debian/manpages/water.1e
@@ -0,0 +1,95 @@
+'\" t
+.\"     Title: WATER
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "WATER" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+water \- Smith\-Waterman local alignment of sequences
+.SH "SYNOPSIS"
+.HP \w'\fBwater\fR\ 'u
+\fBwater\fR \fB\-asequence\ \fR\fB\fIsequence\fR\fR \fB\-bsequence\ \fR\fB\fIseqall\fR\fR [\fB\-datafile\ \fR\fB\fImatrixf\fR\fR] \fB\-gapopen\ \fR\fB\fIfloat\fR\fR \fB\-gapextend\ \fR\fB\fIfloat\fR\fR \fB\-brief\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIalign\fR\fR
+.HP \w'\fBwater\fR\ 'u
+\fBwater\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBwater\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Alignment:Local" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-asequence\fR \fIsequence\fR
+.RS 4
+.RE
+.PP
+\fB\-bsequence\fR \fIseqall\fR
+.RS 4
+.RE
+.PP
+\fB\-datafile\fR \fImatrixf\fR
+.RS 4
+This is the scoring matrix file used when comparing sequences\&. By default it is the file \*(AqEBLOSUM62\*(Aq (for proteins) or the file \*(AqEDNAFULL\*(Aq (for nucleic sequences)\&. These files are found in the \*(Aqdata\*(Aq directory of the EMBOSS installation\&.
+.RE
+.SS "Required section"
+.PP
+\fB\-gapopen\fR \fIfloat\fR
+.RS 4
+The gap open penalty is the score taken away when a gap is created\&. The best value depends on the choice of comparison matrix\&. The default value assumes you are using the EBLOSUM62 matrix for protein sequences, and the EDNAFULL matrix for nucleotide sequences\&. Default value: @($(acdprotein)? 10\&.0 : 10\&.0)
+.RE
+.PP
+\fB\-gapextend\fR \fIfloat\fR
+.RS 4
+The gap extension penalty is added to the standard gap penalty for each base or residue in the gap\&. This is how long gaps are penalized\&. Usually you will expect a few long gaps rather than many short gaps, so the gap extension penalty should be lower than the gap penalty\&. An exception is where one or both sequences are single reads with possible sequencing errors in which case you would expect many single base gaps\&. You can get this result by setting the gap open penalty to zero (or very low) and using the gap extension penalty to control gap scoring\&. Default value: @($(acdprotein)? 0\&.5 : 0\&.5)
+.RE
+.SS "Output section"
+.PP
+\fB\-brief\fR \fIboolean\fR
+.RS 4
+Brief identity and similarity Default value: Y
+.RE
+.PP
+\fB\-outfile\fR \fIalign\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+water is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/dotpath.1e
+++ emboss-6.4.0/debian/manpages/dotpath.1e
@@ -0,0 +1,90 @@
+'\" t
+.\"     Title: DOTPATH
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "DOTPATH" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+dotpath \- Draw a non\-overlapping wordmatch dotplot of two sequences
+.SH "SYNOPSIS"
+.HP \w'\fBdotpath\fR\ 'u
+\fBdotpath\fR \fB\-asequence\ \fR\fB\fIsequence\fR\fR \fB\-bsequence\ \fR\fB\fIsequence\fR\fR \fB\-wordsize\ \fR\fB\fIinteger\fR\fR [\fB\-overlaps\ \fR\fB\fIboolean\fR\fR] [\fB\-boxit\ \fR\fB\fIboolean\fR\fR] \fB\-graph\ \fR\fB\fIgraph\fR\fR
+.HP \w'\fBdotpath\fR\ 'u
+\fBdotpath\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBdotpath\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Alignment:Dot plots" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-asequence\fR \fIsequence\fR
+.RS 4
+.RE
+.PP
+\fB\-bsequence\fR \fIsequence\fR
+.RS 4
+.RE
+.SS "Required section"
+.PP
+\fB\-wordsize\fR \fIinteger\fR
+.RS 4
+Default value: 4
+.RE
+.SS "Output section"
+.PP
+\fB\-overlaps\fR \fIboolean\fR
+.RS 4
+Displays the overlapping matches (in red) as well as the minimal set of non\-overlapping matches Default value: N
+.RE
+.PP
+\fB\-boxit\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-graph\fR \fIgraph\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+dotpath is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/cirdna.1e
+++ emboss-6.4.0/debian/manpages/cirdna.1e
@@ -0,0 +1,167 @@
+'\" t
+.\"     Title: CIRDNA
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "CIRDNA" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+cirdna \- Draws circular maps of DNA constructs
+.SH "SYNOPSIS"
+.HP \w'\fBcirdna\fR\ 'u
+\fBcirdna\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR [\fB\-maxgroups\ \fR\fB\fIinteger\fR\fR] [\fB\-maxlabels\ \fR\fB\fIinteger\fR\fR] \fB\-ruler\ \fR\fB\fIboolean\fR\fR \fB\-blocktype\ \fR\fB\fIlist\fR\fR [\fB\-originangle\ \fR\fB\fIfloat\fR\fR] \fB\-posticks\ \fR\fB\fIselection\fR\fR \fB\-posblocks\ \fR\fB\fIselection\fR\fR [\fB\-intersymbol\ \fR\fB\fIboolean\fR\fR] [\fB\-intercolour\ \fR\fB\fIinteger\fR\fR] [\fB\-interticks\ \fR\fB\fIboolean\fR\fR] [\fB\-gapsize\ \fR\fB\fIinteger\fR\fR] [\fB\-ticklines\ \fR\fB\fIboolean\fR\fR] [\fB\-textheight\ \fR\fB\fIfloat\fR\fR] [\fB\-textlength\ \fR\fB\fIfloat\fR\fR] [\fB\-tickheight\ \fR\fB\fIfloat\fR\fR] [\fB\-blockheight\ \fR\fB\fIfloat\fR\fR] [\fB\-rangeheight\ \fR\fB\fIfloat\fR\fR] [\fB\-gapgroup\ \fR\fB\fIfloat\fR\fR] [\fB\-postext\ \fR\fB\fIfloat\fR\fR] \fB\-graphout\ \fR\fB\fIgraph\fR\fR
+.HP \w'\fBcirdna\fR\ 'u
+\fBcirdna\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBcirdna\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Display" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-infile\fR \fIinfile\fR
+.RS 4
+Default value: inputfile
+.RE
+.SS "Additional section"
+.PP
+\fB\-maxgroups\fR \fIinteger\fR
+.RS 4
+Default value: 20
+.RE
+.PP
+\fB\-maxlabels\fR \fIinteger\fR
+.RS 4
+Default value: 10000
+.RE
+.SS "Output section"
+.PP
+\fB\-ruler\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-blocktype\fR \fIlist\fR
+.RS 4
+Default value: Filled
+.RE
+.PP
+\fB\-originangle\fR \fIfloat\fR
+.RS 4
+Default value: 90
+.RE
+.PP
+\fB\-posticks\fR \fIselection\fR
+.RS 4
+Default value: Out
+.RE
+.PP
+\fB\-posblocks\fR \fIselection\fR
+.RS 4
+Default value: In
+.RE
+.PP
+\fB\-intersymbol\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-intercolour\fR \fIinteger\fR
+.RS 4
+Default value: 1
+.RE
+.PP
+\fB\-interticks\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-gapsize\fR \fIinteger\fR
+.RS 4
+Default value: 500
+.RE
+.PP
+\fB\-ticklines\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-textheight\fR \fIfloat\fR
+.RS 4
+Height of text\&. Enter a number <1\&.0 or >1\&.0 to decrease or increase the size, respectively Default value: 1\&.0
+.RE
+.PP
+\fB\-textlength\fR \fIfloat\fR
+.RS 4
+Length of text\&. Enter a number <1\&.0 or >1\&.0 to decrease or increase the size, respectively Default value: 1\&.0
+.RE
+.PP
+\fB\-tickheight\fR \fIfloat\fR
+.RS 4
+Height of ticks\&. Enter a number <1\&.0 or >1\&.0 to decrease or increase the size, respectively Default value: 1\&.0
+.RE
+.PP
+\fB\-blockheight\fR \fIfloat\fR
+.RS 4
+Height of blocks\&. Enter a number <1\&.0 or >1\&.0 to decrease or increase the size, respectively Default value: 1\&.0
+.RE
+.PP
+\fB\-rangeheight\fR \fIfloat\fR
+.RS 4
+Height of range ends\&. Enter a number <1\&.0 or >1\&.0 to decrease or increase the size, respectively Default value: 1\&.0
+.RE
+.PP
+\fB\-gapgroup\fR \fIfloat\fR
+.RS 4
+Space between groups\&. Enter a number <1\&.0 or >1\&.0 to decrease or increase the size, respectively Default value: 1\&.0
+.RE
+.PP
+\fB\-postext\fR \fIfloat\fR
+.RS 4
+Space between text and ticks, blocks, and ranges\&. Enter a number <1\&.0 or >1\&.0 to decrease or increase the size, respectively Default value: 1\&.0
+.RE
+.PP
+\fB\-graphout\fR \fIgraph\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+cirdna is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/maskambigprot.1e
+++ emboss-6.4.0/debian/manpages/maskambigprot.1e
@@ -0,0 +1,75 @@
+'\" t
+.\"     Title: MASKAMBIGPROT
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "MASKAMBIGPROT" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+maskambigprot \- Masks all ambiguity characters in protein sequences with X
+.SH "SYNOPSIS"
+.HP \w'\fBmaskambigprot\fR\ 'u
+\fBmaskambigprot\fR \fB\-feature\ \fR\fB\fIboolean\fR\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR
+.HP \w'\fBmaskambigprot\fR\ 'u
+\fBmaskambigprot\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBmaskambigprot\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-feature\fR \fIboolean\fR
+.RS 4
+.RE
+.PP
+\fB\-sequence\fR \fIseqall\fR
+.RS 4
+.RE
+.SS "Advanced section"
+.SS "Output section"
+.PP
+\fB\-outseq\fR \fIseqoutall\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+maskambigprot is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/tmap.1e
+++ emboss-6.4.0/debian/manpages/tmap.1e
@@ -0,0 +1,75 @@
+'\" t
+.\"     Title: TMAP
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "TMAP" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+tmap \- Predict and plot transmembrane segments in protein sequences
+.SH "SYNOPSIS"
+.HP \w'\fBtmap\fR\ 'u
+\fBtmap\fR \fB\-sequences\ \fR\fB\fIseqset\fR\fR \fB\-graph\ \fR\fB\fIxygraph\fR\fR \fB\-outfile\ \fR\fB\fIreport\fR\fR
+.HP \w'\fBtmap\fR\ 'u
+\fBtmap\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBtmap\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Protein:Functional sites" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequences\fR \fIseqset\fR
+.RS 4
+File containing a protein sequence alignment
+.RE
+.SS "Output section"
+.PP
+\fB\-graph\fR \fIxygraph\fR
+.RS 4
+.RE
+.PP
+\fB\-outfile\fR \fIreport\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+tmap is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/epestfind.1e
+++ emboss-6.4.0/debian/manpages/epestfind.1e
@@ -0,0 +1,124 @@
+'\" t
+.\"     Title: EPESTFIND
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "EPESTFIND" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+epestfind \- Finds PEST motifs as potential proteolytic cleavage sites
+.SH "SYNOPSIS"
+.HP \w'\fBepestfind\fR\ 'u
+\fBepestfind\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR [\fB\-mwdata\ \fR\fB\fIdatafile\fR\fR] \fB\-window\ \fR\fB\fIinteger\fR\fR \fB\-order\ \fR\fB\fIselection\fR\fR [\fB\-threshold\ \fR\fB\fIfloat\fR\fR] \fB\-mono\ \fR\fB\fIboolean\fR\fR \fB\-potential\ \fR\fB\fIboolean\fR\fR \fB\-poor\ \fR\fB\fIboolean\fR\fR \fB\-invalid\ \fR\fB\fIboolean\fR\fR \fB\-map\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR \fB\-graph\ \fR\fB\fIxygraph\fR\fR
+.HP \w'\fBepestfind\fR\ 'u
+\fBepestfind\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBepestfind\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Protein:Motifs" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIsequence\fR
+.RS 4
+Protein sequence USA to be analysed\&.
+.RE
+.PP
+\fB\-mwdata\fR \fIdatafile\fR
+.RS 4
+Default value: Emolwt\&.dat
+.RE
+.SS "Required section"
+.PP
+\fB\-window\fR \fIinteger\fR
+.RS 4
+Minimal distance between positively charged amino acids\&. Default value: 10
+.RE
+.PP
+\fB\-order\fR \fIselection\fR
+.RS 4
+Name of the output file which holds the results of the analysis\&. Results may be sorted by length, position and score\&. Default value: score
+.RE
+.SS "Additional section"
+.PP
+\fB\-threshold\fR \fIfloat\fR
+.RS 4
+Threshold value to discriminate weak from potential PEST motifs\&. Valid PEST motifs are discriminated into \*(Aqpoor\*(Aq and \*(Aqpotential\*(Aq motifs depending on this threshold score\&. By default, the default value is set to +5\&.0 based on experimental data\&. Alterations are not recommended since significance is a matter of biology, not mathematics\&. Default value: +5\&.0
+.RE
+.SS "Advanced section"
+.PP
+\fB\-mono\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-potential\fR \fIboolean\fR
+.RS 4
+Decide whether potential PEST motifs should be printed\&. Default value: Y
+.RE
+.PP
+\fB\-poor\fR \fIboolean\fR
+.RS 4
+Decide whether poor PEST motifs should be printed\&. Default value: Y
+.RE
+.PP
+\fB\-invalid\fR \fIboolean\fR
+.RS 4
+Decide whether invalid PEST motifs should be printed\&. Default value: N
+.RE
+.PP
+\fB\-map\fR \fIboolean\fR
+.RS 4
+Decide whether PEST motifs should be mapped to sequence\&. Default value: Y
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+Name of file to which results will be written\&.
+.RE
+.PP
+\fB\-graph\fR \fIxygraph\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+epestfind is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/wossparam.1e
+++ emboss-6.4.0/debian/manpages/wossparam.1e
@@ -0,0 +1,139 @@
+'\" t
+.\"     Title: WOSSPARAM
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "WOSSPARAM" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+wossparam \- Finds programs by EDAM parameter
+.SH "SYNOPSIS"
+.HP \w'\fBwossparam\fR\ 'u
+\fBwossparam\fR \fB\-identifier\ \fR\fB\fIstring\fR\fR [\fB\-explode\ \fR\fB\fIboolean\fR\fR] [\fB\-showkeywords\ \fR\fB\fIboolean\fR\fR] \fB\-sensitive\ \fR\fB\fIboolean\fR\fR \fB\-subclasses\ \fR\fB\fIboolean\fR\fR \fB\-obsolete\ \fR\fB\fIboolean\fR\fR \fB\-emboss\ \fR\fB\fIboolean\fR\fR \fB\-embassy\ \fR\fB\fIboolean\fR\fR \fB\-showembassy\ \fR\fB\fIstring\fR\fR \fB\-colon\ \fR\fB\fIboolean\fR\fR \fB\-gui\ \fR\fB\fIboolean\fR\fR [\fB\-outfile\ \fR\fB\fIoutfile\fR\fR] [\fB\-html\ \fR\fB\fItoggle\fR\fR] [\fB\-groups\ \fR\fB\fIboolean\fR\fR] [\fB\-alphabetic\ \fR\fB\fIboolean\fR\fR]
+.HP \w'\fBwossparam\fR\ 'u
+\fBwossparam\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBwossparam\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Ontology:EDAM,Documentation" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-identifier\fR \fIstring\fR
+.RS 4
+.RE
+.SS "Additional section"
+.PP
+\fB\-explode\fR \fIboolean\fR
+.RS 4
+The groups that EMBOSS applications belong to have two forms, exploded and not exploded\&. The exploded group names are more numerous and often vaguely phrased than the non\-exploded ones\&. The exploded names are formed from definitions of the group names that start like NAME1:NAME2 and which are then expanded into many combinations of the names as: \*(AqNAME1\*(Aq, \*(AqNAME2\*(Aq, \*(AqNAME1 NAME2\*(Aq, NAME2 NAME1\*(Aq\&. The non\-expanded names are simply like: \*(AqNAME1 NAME2\*(Aq\&. Default value: N
+.RE
+.PP
+\fB\-showkeywords\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.SS "Advanced section"
+.PP
+\fB\-sensitive\fR \fIboolean\fR
+.RS 4
+By default, the query keywords are matched against the EDAM term names (and synonyms) only\&. This option also matches the keywords against the EDAM term definitions and will therefore (typically) report more matches\&. Default value: N
+.RE
+.PP
+\fB\-subclasses\fR \fIboolean\fR
+.RS 4
+Extend the query matches to include all terms which are specialisations (EDAM sub\-classes) of the matched type\&. Default value: Y
+.RE
+.PP
+\fB\-obsolete\fR \fIboolean\fR
+.RS 4
+The default behaviour is to not use or return obsolete terms\&. This option if set will include all terms\&. Default value: N
+.RE
+.PP
+\fB\-emboss\fR \fIboolean\fR
+.RS 4
+If you use this option then EMBOSS program documentation will be searched\&. If this option is set to be false, then only the EMBASSY programs will be searched (if the \-embassy option is true)\&. EMBASSY programs are not strictly part of EMBOSS, but use the same code libraries and share the same look and feel, but are generally developed by people who wish the programs to be outside of the GNU Public Licence scheme Default value: Y
+.RE
+.PP
+\fB\-embassy\fR \fIboolean\fR
+.RS 4
+If you use this option then EMBASSY program documentation will be searched\&. If this option is set to be false, then only the EMBOSS programs will be searched (if the \-emboss option is true)\&. EMBASSY programs are not strictly part of EMBOSS, but use the same code libraries and share the same look and feel, but are generally developed by people who wish the programs to be outside of the GNU Public Licence scheme Default value: Y
+.RE
+.PP
+\fB\-showembassy\fR \fIstring\fR
+.RS 4
+If you use this option then this EMBASSY package program documentation will be searched\&. EMBASSY programs are not strictly part of EMBOSS, but use the same code libraries and share the same look and feel, but are generally developed by people who wish the programs to be outside of the GNU Public Licence scheme
+.RE
+.PP
+\fB\-colon\fR \fIboolean\fR
+.RS 4
+The groups that EMBOSS applications belong to up to two levels, for example the primary group \*(AqALIGNMENT\*(Aq has several sub\-groups, or second\-level groups, e\&.g\&.: CONSENSUS, DIFFERENCES, DOT PLOTS, GLOBAL, LOCAL, MULTIPLE\&. To aid programs that parse the output of wossname that require the names of these subgroups, a colon \*(Aq:\*(Aq will be placed between the first and second level of the group name if this option is true\&. Note: This does not apply if the group names have been exploded with the \*(Aqexplode\*(Aq option\&. Default value: N
+.RE
+.PP
+\fB\-gui\fR \fIboolean\fR
+.RS 4
+This option is intended to help those who are designing Graphical User Interfaces to the EMBOSS applications\&. Some EMBOSS programs are inappropriate for running in a GUI, these include other menu programs and interactive editors\&. This option allows you to only report those programs that can be run from a GUI Default value: N
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+Default value: stdout
+.RE
+.SS "Html section"
+.PP
+\fB\-html\fR \fItoggle\fR
+.RS 4
+If you are sending the output to a file, this will format it for displaying as a table in a WWW document\&. Default value: N
+.RE
+.PP
+\fB\-groups\fR \fIboolean\fR
+.RS 4
+If you use this option, then only the group names will be output to the file Default value: N
+.RE
+.PP
+\fB\-alphabetic\fR \fIboolean\fR
+.RS 4
+If you use this option, then you will get a single list of the program names and descriptions instead of the programs being listed in their functional groups\&. Default value: N
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+wossparam is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/dottup.1e
+++ emboss-6.4.0/debian/manpages/dottup.1e
@@ -0,0 +1,94 @@
+'\" t
+.\"     Title: DOTTUP
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "DOTTUP" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+dottup \- Displays a wordmatch dotplot of two sequences
+.SH "SYNOPSIS"
+.HP \w'\fBdottup\fR\ 'u
+\fBdottup\fR \fB\-asequence\ \fR\fB\fIsequence\fR\fR \fB\-bsequence\ \fR\fB\fIsequence\fR\fR \fB\-wordsize\ \fR\fB\fIinteger\fR\fR \fB\-stretch\ \fR\fB\fItoggle\fR\fR \fB\-graph\ \fR\fB\fIgraph\fR\fR \fB\-xygraph\ \fR\fB\fIxygraph\fR\fR \fB\-boxit\ \fR\fB\fIboolean\fR\fR
+.HP \w'\fBdottup\fR\ 'u
+\fBdottup\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBdottup\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Alignment:Dot plots" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-asequence\fR \fIsequence\fR
+.RS 4
+.RE
+.PP
+\fB\-bsequence\fR \fIsequence\fR
+.RS 4
+.RE
+.SS "Required section"
+.PP
+\fB\-wordsize\fR \fIinteger\fR
+.RS 4
+Default value: 10
+.RE
+.SS "Output section"
+.PP
+\fB\-stretch\fR \fItoggle\fR
+.RS 4
+Use non\-proportional axes Default value: N
+.RE
+.PP
+\fB\-graph\fR \fIgraph\fR
+.RS 4
+.RE
+.PP
+\fB\-xygraph\fR \fIxygraph\fR
+.RS 4
+.RE
+.PP
+\fB\-boxit\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+dottup is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/ontotext.1e
+++ emboss-6.4.0/debian/manpages/ontotext.1e
@@ -0,0 +1,82 @@
+'\" t
+.\"     Title: ONTOTEXT
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "ONTOTEXT" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+ontotext \- Get ontology term(s) original full text
+.SH "SYNOPSIS"
+.HP \w'\fBontotext\fR\ 'u
+\fBontotext\fR \fB\-oboterms\ \fR\fB\fIobo\fR\fR [\fB\-subclasses\ \fR\fB\fIboolean\fR\fR] [\fB\-obsolete\ \fR\fB\fIboolean\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBontotext\fR\ 'u
+\fBontotext\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBontotext\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Ontology,Data retrieval:Ontology data,Data retrieval:Text data" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-oboterms\fR \fIobo\fR
+.RS 4
+.RE
+.SS "Additional section"
+.PP
+\fB\-subclasses\fR \fIboolean\fR
+.RS 4
+Extend the query matches to include all terms which are specialisations (sub\-classes) of the matched terms\&. Default value: N
+.RE
+.PP
+\fB\-obsolete\fR \fIboolean\fR
+.RS 4
+The default behaviour is to not use or return obsolete terms\&. This option if set will include all terms\&. Default value: N
+.RE
+.SS "Advanced section"
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+ontotext is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/nohtml.1e
+++ emboss-6.4.0/debian/manpages/nohtml.1e
@@ -0,0 +1,73 @@
+'\" t
+.\"     Title: NOHTML
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "NOHTML" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+nohtml \- Remove mark\-up (e\&.g\&. HTML tags) from an ASCII text file
+.SH "SYNOPSIS"
+.HP \w'\fBnohtml\fR\ 'u
+\fBnohtml\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBnohtml\fR\ 'u
+\fBnohtml\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBnohtml\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-infile\fR \fIinfile\fR
+.RS 4
+.RE
+.SS "Required section"
+.SS "Additional section"
+.SS "Advanced section"
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+nohtml is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/compseq.1e
+++ emboss-6.4.0/debian/manpages/compseq.1e
@@ -0,0 +1,108 @@
+'\" t
+.\"     Title: COMPSEQ
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "COMPSEQ" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+compseq \- Calculate the composition of unique words in sequences
+.SH "SYNOPSIS"
+.HP \w'\fBcompseq\fR\ 'u
+\fBcompseq\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR [\fB\-infile\ \fR\fB\fIinfile\fR\fR] \fB\-word\ \fR\fB\fIinteger\fR\fR [\fB\-frame\ \fR\fB\fIinteger\fR\fR] \fB\-ignorebz\ \fR\fB\fIboolean\fR\fR \fB\-reverse\ \fR\fB\fIboolean\fR\fR [\fB\-calcfreq\ \fR\fB\fIboolean\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-zerocount\ \fR\fB\fIboolean\fR\fR]
+.HP \w'\fBcompseq\fR\ 'u
+\fBcompseq\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBcompseq\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Composition,Protein:Composition" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqall\fR
+.RS 4
+.RE
+.PP
+\fB\-infile\fR \fIinfile\fR
+.RS 4
+This is a file previously produced by \*(Aqcompseq\*(Aq that can be used to set the expected frequencies of words in this analysis\&. The word size in the current run must be the same as the one in this results file\&. Obviously, you should use a file produced from protein sequences if you are counting protein sequence word frequencies, and you must use one made from nucleotide frequencies if you are analysing a nucleotide sequence\&.
+.RE
+.SS "Required section"
+.PP
+\fB\-word\fR \fIinteger\fR
+.RS 4
+This is the size of word (n\-mer) to count\&. Thus if you want to count codon frequencies for a nucleotide sequence, you should enter 3 here\&. Default value: 2
+.RE
+.SS "Additional section"
+.PP
+\fB\-frame\fR \fIinteger\fR
+.RS 4
+The normal behaviour of \*(Aqcompseq\*(Aq is to count the frequencies of all words that occur by moving a window of length \*(Aqword\*(Aq up by one each time\&. This option allows you to move the window up by the length of the word each time, skipping over the intervening words\&. You can count only those words that occur in a single frame of the word by setting this value to a number other than zero\&. If you set it to 1 it will only count the words in frame 1, 2 will only count the words in frame 2 and so on\&.
+.RE
+.PP
+\fB\-ignorebz\fR \fIboolean\fR
+.RS 4
+The amino acid code B represents Asparagine or Aspartic acid and the code Z represents Glutamine or Glutamic acid\&. These are not commonly used codes and you may wish not to count words containing them, just noting them in the count of \*(AqOther\*(Aq words\&. Default value: Y
+.RE
+.PP
+\fB\-reverse\fR \fIboolean\fR
+.RS 4
+Set this to be true if you also wish to also count words in the reverse complement of a nucleic sequence\&. Default value: N
+.RE
+.PP
+\fB\-calcfreq\fR \fIboolean\fR
+.RS 4
+If this is set true then the expected frequencies of words are calculated from the observed frequency of single bases or residues in the sequences\&. If you are reporting a word size of 1 (single bases or residues) then there is no point in using this option because the calculated expected frequency will be equal to the observed frequency\&. Calculating the expected frequencies like this will give an approximation of the expected frequencies that you might get by using an input file of frequencies produced by a previous run of this program\&. If an input file of expected word frequencies has been specified then the values from that file will be used instead of this calculation of expected frequency from the sequence, even if \*(Aqcalcfreq\*(Aq is set to be true\&. Default value: N
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+This is the results file\&.
+.RE
+.PP
+\fB\-zerocount\fR \fIboolean\fR
+.RS 4
+You can make the output results file much smaller if you do not display the words with a zero count\&. Default value: Y
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+compseq is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/taxgetdown.1e
+++ emboss-6.4.0/debian/manpages/taxgetdown.1e
@@ -0,0 +1,73 @@
+'\" t
+.\"     Title: TAXGETDOWN
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "TAXGETDOWN" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+taxgetdown \- Get descendants of taxon(s)
+.SH "SYNOPSIS"
+.HP \w'\fBtaxgetdown\fR\ 'u
+\fBtaxgetdown\fR \fB\-taxons\ \fR\fB\fItaxon\fR\fR \fB\-outfile\ \fR\fB\fIouttaxon\fR\fR
+.HP \w'\fBtaxgetdown\fR\ 'u
+\fBtaxgetdown\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBtaxgetdown\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Ontology:Taxonomy" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-taxons\fR \fItaxon\fR
+.RS 4
+.RE
+.SS "Required section"
+.SS "Additional section"
+.SS "Advanced section"
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIouttaxon\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+taxgetdown is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/pepcoil.1e
+++ emboss-6.4.0/debian/manpages/pepcoil.1e
@@ -0,0 +1,91 @@
+'\" t
+.\"     Title: PEPCOIL
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "PEPCOIL" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+pepcoil \- Predicts coiled coil regions in protein sequences
+.SH "SYNOPSIS"
+.HP \w'\fBpepcoil\fR\ 'u
+\fBpepcoil\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-window\ \fR\fB\fIinteger\fR\fR \fB\-coil\ \fR\fB\fIboolean\fR\fR \fB\-frame\ \fR\fB\fIboolean\fR\fR \fB\-other\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIreport\fR\fR
+.HP \w'\fBpepcoil\fR\ 'u
+\fBpepcoil\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBpepcoil\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Protein:2D Structure,Protein:Domains" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqall\fR
+.RS 4
+.RE
+.SS "Required section"
+.PP
+\fB\-window\fR \fIinteger\fR
+.RS 4
+Default value: 28
+.RE
+.SS "Output section"
+.PP
+\fB\-coil\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-frame\fR \fIboolean\fR
+.RS 4
+Default value: $(coil)
+.RE
+.PP
+\fB\-other\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-outfile\fR \fIreport\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+pepcoil is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/cutgextract.1e
+++ emboss-6.4.0/debian/manpages/cutgextract.1e
@@ -0,0 +1,96 @@
+'\" t
+.\"     Title: CUTGEXTRACT
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "CUTGEXTRACT" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+cutgextract \- Extract codon usage tables from CUTG database
+.SH "SYNOPSIS"
+.HP \w'\fBcutgextract\fR\ 'u
+\fBcutgextract\fR \fB\-directory\ \fR\fB\fIdirlist\fR\fR \fB\-release\ \fR\fB\fIstring\fR\fR \fB\-wildspec\ \fR\fB\fIstring\fR\fR \fB\-species\ \fR\fB\fIstring\fR\fR \fB\-allrecords\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR \fB\-filename\ \fR\fB\fIstring\fR\fR
+.HP \w'\fBcutgextract\fR\ 'u
+\fBcutgextract\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBcutgextract\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Database creation" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-directory\fR \fIdirlist\fR
+.RS 4
+.RE
+.SS "Required section"
+.SS "Advanced section"
+.PP
+\fB\-release\fR \fIstring\fR
+.RS 4
+.RE
+.PP
+\fB\-wildspec\fR \fIstring\fR
+.RS 4
+Default value: *\&.codon
+.RE
+.PP
+\fB\-species\fR \fIstring\fR
+.RS 4
+Default value: *
+.RE
+.PP
+\fB\-allrecords\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.PP
+\fB\-filename\fR \fIstring\fR
+.RS 4
+Single output filename to override automatic one file for each species\&. Leave blank to generate the filenames\&. Specify a filename to combine several species into one file\&.
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+cutgextract is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/treetypedisplay.1e
+++ emboss-6.4.0/debian/manpages/treetypedisplay.1e
@@ -0,0 +1,65 @@
+'\" t
+.\"     Title: TREETYPEDISPLAY
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "TREETYPEDISPLAY" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+treetypedisplay \- Test of graphics
+.SH "SYNOPSIS"
+.HP \w'\fBtreetypedisplay\fR\ 'u
+\fBtreetypedisplay\fR \fB\-graph\ \fR\fB\fIgraph\fR\fR
+.HP \w'\fBtreetypedisplay\fR\ 'u
+\fBtreetypedisplay\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBtreetypedisplay\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Test" command group(s)\&.
+.SH "OPTIONS"
+.SS "Output section"
+.PP
+\fB\-graph\fR \fIgraph\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+treetypedisplay is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/seqretsingle.1e
+++ emboss-6.4.0/debian/manpages/seqretsingle.1e
@@ -0,0 +1,74 @@
+'\" t
+.\"     Title: SEQRETSINGLE
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "SEQRETSINGLE" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+seqretsingle \- Reads and writes (returns) a single sequence
+.SH "SYNOPSIS"
+.HP \w'\fBseqretsingle\fR\ 'u
+\fBseqretsingle\fR \fB\-feature\ \fR\fB\fIboolean\fR\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR \fB\-outseq\ \fR\fB\fIseqout\fR\fR
+.HP \w'\fBseqretsingle\fR\ 'u
+\fBseqretsingle\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBseqretsingle\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Test" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-feature\fR \fIboolean\fR
+.RS 4
+.RE
+.PP
+\fB\-sequence\fR \fIsequence\fR
+.RS 4
+.RE
+.SS "Output section"
+.PP
+\fB\-outseq\fR \fIseqout\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+seqretsingle is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/skipredundant.1e
+++ emboss-6.4.0/debian/manpages/skipredundant.1e
@@ -0,0 +1,116 @@
+'\" t
+.\"     Title: SKIPREDUNDANT
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "SKIPREDUNDANT" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+skipredundant \- Remove redundant sequences from an input set
+.SH "SYNOPSIS"
+.HP \w'\fBskipredundant\fR\ 'u
+\fBskipredundant\fR \fB\-feature\ \fR\fB\fItoggle\fR\fR \fB\-sequences\ \fR\fB\fIseqset\fR\fR [\fB\-datafile\ \fR\fB\fImatrixf\fR\fR] \fB\-mode\ \fR\fB\fIlist\fR\fR \fB\-threshold\ \fR\fB\fIfloat\fR\fR \fB\-minthreshold\ \fR\fB\fIfloat\fR\fR \fB\-maxthreshold\ \fR\fB\fIfloat\fR\fR \fB\-gapopen\ \fR\fB\fIfloat\fR\fR \fB\-gapextend\ \fR\fB\fIfloat\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR \fB\-redundantoutseq\ \fR\fB\fIseqoutall\fR\fR
+.HP \w'\fBskipredundant\fR\ 'u
+\fBskipredundant\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBskipredundant\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-feature\fR \fItoggle\fR
+.RS 4
+Sequence feature information will be retained if this option is set\&.
+.RE
+.PP
+\fB\-sequences\fR \fIseqset\fR
+.RS 4
+.RE
+.PP
+\fB\-datafile\fR \fImatrixf\fR
+.RS 4
+This is the scoring matrix file used when comparing sequences\&. By default it is the file \*(AqEBLOSUM62\*(Aq (for proteins) or the file \*(AqEDNAFULL\*(Aq (for nucleic sequences)\&. These files are found in the \*(Aqdata\*(Aq directory of the EMBOSS installation\&.
+.RE
+.SS "Required section"
+.PP
+\fB\-mode\fR \fIlist\fR
+.RS 4
+This option specifies whether to remove redundancy at a single threshold percentage sequence similarity or remove redundancy outside a range of acceptable threshold percentage similarity\&. All permutations of pair\-wise sequence alignments are calculated for each set of input sequences in turn using the EMBOSS implementation of the Needleman and Wunsch global alignment algorithm\&. Redundant sequences are removed in one of two modes as follows: (i) If a pair of proteins achieve greater than a threshold percentage sequence similarity (specified by the user) the shortest sequence is discarded\&. (ii) If a pair of proteins have a percentage sequence similarity that lies outside an acceptable range (specified by the user) the shortest sequence is discarded\&. Default value: 1
+.RE
+.PP
+\fB\-threshold\fR \fIfloat\fR
+.RS 4
+This option specifies the percentage sequence identity redundancy threshold\&. The percentage sequence identity redundancy threshold determines the redundancy calculation\&. If a pair of proteins achieve greater than this threshold the shortest sequence is discarded\&. Default value: 95\&.0
+.RE
+.PP
+\fB\-minthreshold\fR \fIfloat\fR
+.RS 4
+This option specifies the percentage sequence identity redundancy threshold (lower limit)\&. The percentage sequence identity redundancy threshold determines the redundancy calculation\&. If a pair of proteins have a percentage sequence similarity that lies outside an acceptable range the shortest sequence is discarded\&. Default value: 30\&.0
+.RE
+.PP
+\fB\-maxthreshold\fR \fIfloat\fR
+.RS 4
+This option specifies the percentage sequence identity redundancy threshold (upper limit)\&. The percentage sequence identity redundancy threshold determines the redundancy calculation\&. If a pair of proteins have a percentage sequence similarity that lies outside an acceptable range the shortest sequence is discarded\&. Default value: 90\&.0
+.RE
+.PP
+\fB\-gapopen\fR \fIfloat\fR
+.RS 4
+The gap open penalty is the score taken away when a gap is created\&. The best value depends on the choice of comparison matrix\&. The default value assumes you are using the EBLOSUM62 matrix for protein sequences, and the EDNAFULL matrix for nucleotide sequences\&. Default value: @($(acdprotein)? 10\&.0 : 10\&.0 )
+.RE
+.PP
+\fB\-gapextend\fR \fIfloat\fR
+.RS 4
+The gap extension, penalty is added to the standard gap penalty for each base or residue in the gap\&. This is how long gaps are penalized\&. Usually you will expect a few long gaps rather than many short gaps, so the gap extension penalty should be lower than the gap penalty\&. An exception is where one or both sequences are single reads with possible sequencing errors in which case you would expect many single base gaps\&. You can get this result by setting the gap open penalty to zero (or very low) and using the gap extension penalty to control gap scoring\&. Default value: @($(acdprotein)? 0\&.5 : 0\&.5 )
+.RE
+.SS "Advanced section"
+.SS "Output section"
+.PP
+\fB\-outseq\fR \fIseqoutall\fR
+.RS 4
+.RE
+.PP
+\fB\-redundantoutseq\fR \fIseqoutall\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+skipredundant is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/recoder.1e
+++ emboss-6.4.0/debian/manpages/recoder.1e
@@ -0,0 +1,86 @@
+'\" t
+.\"     Title: RECODER
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "RECODER" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+recoder \- Find restriction sites to remove (mutate) with no translation change
+.SH "SYNOPSIS"
+.HP \w'\fBrecoder\fR\ 'u
+\fBrecoder\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR \fB\-enzymes\ \fR\fB\fIstring\fR\fR \fB\-sshow\ \fR\fB\fIboolean\fR\fR \fB\-tshow\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIreport\fR\fR
+.HP \w'\fBrecoder\fR\ 'u
+\fBrecoder\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBrecoder\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Restriction" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIsequence\fR
+.RS 4
+.RE
+.SS "Required section"
+.PP
+\fB\-enzymes\fR \fIstring\fR
+.RS 4
+Default value: all
+.RE
+.SS "Output section"
+.PP
+\fB\-sshow\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-tshow\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-outfile\fR \fIreport\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+recoder is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/domtestb.1e
+++ emboss-6.4.0/debian/manpages/domtestb.1e
@@ -0,0 +1,65 @@
+'\" t
+.\"     Title: DOMTESTB
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "DOMTESTB" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+domtestb \- Create, manipulate and write out XML
+.SH "SYNOPSIS"
+.HP \w'\fBdomtestb\fR\ 'u
+\fBdomtestb\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBdomtestb\fR\ 'u
+\fBdomtestb\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBdomtestb\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&.
+.SH "OPTIONS"
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+domtestb is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/primers.1e
+++ emboss-6.4.0/debian/manpages/primers.1e
@@ -0,0 +1,102 @@
+'\" t
+.\"     Title: PRIMERS
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "PRIMERS" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+primers \- Simple version of primer3 to pick PCR primers
+.SH "SYNOPSIS"
+.HP \w'\fBprimers\fR\ 'u
+\fBprimers\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR [\fB\-targetregion\ \fR\fB\fIrange\fR\fR] [\fB\-minsize\ \fR\fB\fIinteger\fR\fR] [\fB\-maxsize\ \fR\fB\fIinteger\fR\fR] [\fB\-maxdifftm\ \fR\fB\fIfloat\fR\fR] [\fB\-explainflag\ \fR\fB\fIboolean\fR\fR] [\fB\-numreturn\ \fR\fB\fIinteger\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBprimers\fR\ 'u
+\fBprimers\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBprimers\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Primers" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqall\fR
+.RS 4
+The sequence from which to choose primers\&. The sequence must be presented 5\*(Aq \-> 3\*(Aq
+.RE
+.SS "Additional section"
+.PP
+\fB\-targetregion\fR \fIrange\fR
+.RS 4
+If one or more Targets is specified then a legal primer pair must flank at least one of them\&. A Target might be a simple sequence repeat site (for example a CA repeat) or a single\-base\-pair polymorphism\&. The value should be a space\-separated list of <start>,<end> pairs where <start> is the index of the first base of a Target, and <end> is the last E\&.g\&. 50,51 requires primers to surround the 2 bases at positions 50 and 51\&.
+.RE
+.PP
+\fB\-minsize\fR \fIinteger\fR
+.RS 4
+Minimum acceptable length of a primer\&. Must be greater than 0 and less than or equal to MAX\-SIZE\&. Default value: 18
+.RE
+.PP
+\fB\-maxsize\fR \fIinteger\fR
+.RS 4
+Maximum acceptable length (in bases) of a primer\&. Currently this parameter cannot be larger than 35\&. This limit is governed by the maximum oligo size for which Primer3\*(Aqs melting\-temperature is valid\&. Default value: 27
+.RE
+.PP
+\fB\-maxdifftm\fR \fIfloat\fR
+.RS 4
+Maximum acceptable (unsigned) difference between the melting temperatures of the forward and reverse primers\&. Default value: 100\&.0
+.RE
+.SS "Output section"
+.PP
+\fB\-explainflag\fR \fIboolean\fR
+.RS 4
+If this flag is non\-0, produce LEFT\-EXPLAIN and RIGHT\-EXPLAIN, output, which are intended to provide information on the number of primer pairs that Primer3 examined, and statistics on the number discarded for various reasons\&. Default value: N
+.RE
+.PP
+\fB\-numreturn\fR \fIinteger\fR
+.RS 4
+The maximum number of primer pairs to return\&. Primer pairs returned are sorted by their \*(Aqquality\*(Aq, in other words by the value of the objective function (where a lower number indicates a better primer pair)\&. Caution: setting this parameter to a large value will increase running time\&. Default value: 5
+.RE
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+primers is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/finddb.1e
+++ emboss-6.4.0/debian/manpages/finddb.1e
@@ -0,0 +1,93 @@
+'\" t
+.\"     Title: FINDDB
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.75.2 <http://docbook.sf.net/>
+.\"      Date: 07/20/2010
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.3.1
+.\"  Language: English
+.\"
+.TH "FINDDB" "1e" "07/20/2010" "EMBOSS 6.3.1" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+finddb \- Search for a database by keyword
+.SH "SYNOPSIS"
+.HP \w'\fBfinddb\fR\ 'u
+\fBfinddb\fR [\fB\-keyword\ \fR\fB\fIstring\fR\fR] [\fB\-all\ \fR\fB\fItoggle\fR\fR] [\fB\-name\ \fR\fB\fIboolean\fR\fR] [\fB\-server\ \fR\fB\fIboolean\fR\fR] [\fB\-desc\ \fR\fB\fIboolean\fR\fR] [\fB\-outfile\ \fR\fB\fIoutfile\fR\fR]
+.HP \w'\fBfinddb\fR\ 'u
+\fBfinddb\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBfinddb\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Display,Information" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-keyword\fR \fIstring\fR
+.RS 4
+.RE
+.SS "Additional section"
+.PP
+\fB\-all\fR \fItoggle\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-name\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-server\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-desc\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.SS "Advanced section"
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+Default value: stdout
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+finddb is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/wossinput.1e
+++ emboss-6.4.0/debian/manpages/wossinput.1e
@@ -0,0 +1,139 @@
+'\" t
+.\"     Title: WOSSINPUT
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "WOSSINPUT" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+wossinput \- Finds programs by EDAM input data
+.SH "SYNOPSIS"
+.HP \w'\fBwossinput\fR\ 'u
+\fBwossinput\fR \fB\-identifier\ \fR\fB\fIstring\fR\fR [\fB\-explode\ \fR\fB\fIboolean\fR\fR] [\fB\-showkeywords\ \fR\fB\fIboolean\fR\fR] \fB\-sensitive\ \fR\fB\fIboolean\fR\fR \fB\-subclasses\ \fR\fB\fIboolean\fR\fR \fB\-obsolete\ \fR\fB\fIboolean\fR\fR \fB\-emboss\ \fR\fB\fIboolean\fR\fR \fB\-embassy\ \fR\fB\fIboolean\fR\fR \fB\-showembassy\ \fR\fB\fIstring\fR\fR \fB\-colon\ \fR\fB\fIboolean\fR\fR \fB\-gui\ \fR\fB\fIboolean\fR\fR [\fB\-outfile\ \fR\fB\fIoutfile\fR\fR] [\fB\-html\ \fR\fB\fItoggle\fR\fR] [\fB\-groups\ \fR\fB\fIboolean\fR\fR] [\fB\-alphabetic\ \fR\fB\fIboolean\fR\fR]
+.HP \w'\fBwossinput\fR\ 'u
+\fBwossinput\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBwossinput\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Ontology:EDAM,Documentation" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-identifier\fR \fIstring\fR
+.RS 4
+.RE
+.SS "Additional section"
+.PP
+\fB\-explode\fR \fIboolean\fR
+.RS 4
+The groups that EMBOSS applications belong to have two forms, exploded and not exploded\&. The exploded group names are more numerous and often vaguely phrased than the non\-exploded ones\&. The exploded names are formed from definitions of the group names that start like NAME1:NAME2 and which are then expanded into many combinations of the names as: \*(AqNAME1\*(Aq, \*(AqNAME2\*(Aq, \*(AqNAME1 NAME2\*(Aq, NAME2 NAME1\*(Aq\&. The non\-expanded names are simply like: \*(AqNAME1 NAME2\*(Aq\&. Default value: N
+.RE
+.PP
+\fB\-showkeywords\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.SS "Advanced section"
+.PP
+\fB\-sensitive\fR \fIboolean\fR
+.RS 4
+By default, the query keywords are matched against the EDAM term names (and synonyms) only\&. This option also matches the keywords against the EDAM term definitions and will therefore (typically) report more matches\&. Default value: N
+.RE
+.PP
+\fB\-subclasses\fR \fIboolean\fR
+.RS 4
+Extend the query matches to include all terms which are specialisations (EDAM sub\-classes) of the matched type\&. Default value: Y
+.RE
+.PP
+\fB\-obsolete\fR \fIboolean\fR
+.RS 4
+The default behaviour is to not use or return obsolete terms\&. This option if set will include all terms\&. Default value: N
+.RE
+.PP
+\fB\-emboss\fR \fIboolean\fR
+.RS 4
+If you use this option then EMBOSS program documentation will be searched\&. If this option is set to be false, then only the EMBASSY programs will be searched (if the \-embassy option is true)\&. EMBASSY programs are not strictly part of EMBOSS, but use the same code libraries and share the same look and feel, but are generally developed by people who wish the programs to be outside of the GNU Public Licence scheme Default value: Y
+.RE
+.PP
+\fB\-embassy\fR \fIboolean\fR
+.RS 4
+If you use this option then EMBASSY program documentation will be searched\&. If this option is set to be false, then only the EMBOSS programs will be searched (if the \-emboss option is true)\&. EMBASSY programs are not strictly part of EMBOSS, but use the same code libraries and share the same look and feel, but are generally developed by people who wish the programs to be outside of the GNU Public Licence scheme Default value: Y
+.RE
+.PP
+\fB\-showembassy\fR \fIstring\fR
+.RS 4
+If you use this option then this EMBASSY package program documentation will be searched\&. EMBASSY programs are not strictly part of EMBOSS, but use the same code libraries and share the same look and feel, but are generally developed by people who wish the programs to be outside of the GNU Public Licence scheme
+.RE
+.PP
+\fB\-colon\fR \fIboolean\fR
+.RS 4
+The groups that EMBOSS applications belong to up to two levels, for example the primary group \*(AqALIGNMENT\*(Aq has several sub\-groups, or second\-level groups, e\&.g\&.: CONSENSUS, DIFFERENCES, DOT PLOTS, GLOBAL, LOCAL, MULTIPLE\&. To aid programs that parse the output of wossname that require the names of these subgroups, a colon \*(Aq:\*(Aq will be placed between the first and second level of the group name if this option is true\&. Note: This does not apply if the group names have been exploded with the \*(Aqexplode\*(Aq option\&. Default value: N
+.RE
+.PP
+\fB\-gui\fR \fIboolean\fR
+.RS 4
+This option is intended to help those who are designing Graphical User Interfaces to the EMBOSS applications\&. Some EMBOSS programs are inappropriate for running in a GUI, these include other menu programs and interactive editors\&. This option allows you to only report those programs that can be run from a GUI Default value: N
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+Default value: stdout
+.RE
+.SS "Html section"
+.PP
+\fB\-html\fR \fItoggle\fR
+.RS 4
+If you are sending the output to a file, this will format it for displaying as a table in a WWW document\&. Default value: N
+.RE
+.PP
+\fB\-groups\fR \fIboolean\fR
+.RS 4
+If you use this option, then only the group names will be output to the file Default value: N
+.RE
+.PP
+\fB\-alphabetic\fR \fIboolean\fR
+.RS 4
+If you use this option, then you will get a single list of the program names and descriptions instead of the programs being listed in their functional groups\&. Default value: N
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+wossinput is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/dbiflat.1e
+++ emboss-6.4.0/debian/manpages/dbiflat.1e
@@ -0,0 +1,130 @@
+'\" t
+.\"     Title: DBIFLAT
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "DBIFLAT" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+dbiflat \- Index a flat file database
+.SH "SYNOPSIS"
+.HP \w'\fBdbiflat\fR\ 'u
+\fBdbiflat\fR \fB\-dbname\ \fR\fB\fIstring\fR\fR \fB\-idformat\ \fR\fB\fIlist\fR\fR \fB\-directory\ \fR\fB\fIdirectory\fR\fR \fB\-filenames\ \fR\fB\fIstring\fR\fR \fB\-release\ \fR\fB\fIstring\fR\fR \fB\-date\ \fR\fB\fIstring\fR\fR \fB\-fields\ \fR\fB\fIlist\fR\fR \fB\-exclude\ \fR\fB\fIstring\fR\fR \fB\-maxindex\ \fR\fB\fIinteger\fR\fR \fB\-sortoptions\ \fR\fB\fIstring\fR\fR \fB\-systemsort\ \fR\fB\fIboolean\fR\fR \fB\-cleanup\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR \fB\-indexoutdir\ \fR\fB\fIoutdir\fR\fR
+.HP \w'\fBdbiflat\fR\ 'u
+\fBdbiflat\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBdbiflat\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Database indexing" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-dbname\fR \fIstring\fR
+.RS 4
+.RE
+.PP
+\fB\-idformat\fR \fIlist\fR
+.RS 4
+Default value: SWISS
+.RE
+.PP
+\fB\-directory\fR \fIdirectory\fR
+.RS 4
+Default value: \&.
+.RE
+.PP
+\fB\-filenames\fR \fIstring\fR
+.RS 4
+Default value: *\&.dat
+.RE
+.SS "Required section"
+.PP
+\fB\-release\fR \fIstring\fR
+.RS 4
+Default value: 0\&.0
+.RE
+.PP
+\fB\-date\fR \fIstring\fR
+.RS 4
+Default value: 00/00/00
+.RE
+.SS "Advanced section"
+.PP
+\fB\-fields\fR \fIlist\fR
+.RS 4
+Default value: acc
+.RE
+.PP
+\fB\-exclude\fR \fIstring\fR
+.RS 4
+.RE
+.PP
+\fB\-maxindex\fR \fIinteger\fR
+.RS 4
+.RE
+.PP
+\fB\-sortoptions\fR \fIstring\fR
+.RS 4
+Sort options, typically \*(Aq\-T \&.\*(Aq to use current directory for work files and \*(Aq\-k 1,1\*(Aq to force GNU sort to use the first field Default value: \-T \&. \-k 1,1
+.RE
+.PP
+\fB\-systemsort\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-cleanup\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.PP
+\fB\-indexoutdir\fR \fIoutdir\fR
+.RS 4
+Default value: \&.
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+dbiflat is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/prophet.1e
+++ emboss-6.4.0/debian/manpages/prophet.1e
@@ -0,0 +1,85 @@
+'\" t
+.\"     Title: PROPHET
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "PROPHET" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+prophet \- Scan one or more sequences with a Gribskov or Henikoff profile
+.SH "SYNOPSIS"
+.HP \w'\fBprophet\fR\ 'u
+\fBprophet\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR \fB\-gapopen\ \fR\fB\fIfloat\fR\fR \fB\-gapextend\ \fR\fB\fIfloat\fR\fR \fB\-outfile\ \fR\fB\fIalign\fR\fR
+.HP \w'\fBprophet\fR\ 'u
+\fBprophet\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBprophet\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Profiles,Protein:Profiles" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqall\fR
+.RS 4
+.RE
+.PP
+\fB\-infile\fR \fIinfile\fR
+.RS 4
+.RE
+.SS "Required section"
+.PP
+\fB\-gapopen\fR \fIfloat\fR
+.RS 4
+Default value: 1\&.0
+.RE
+.PP
+\fB\-gapextend\fR \fIfloat\fR
+.RS 4
+Default value: 1\&.0
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIalign\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+prophet is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/entrytax.1e
+++ emboss-6.4.0/debian/manpages/entrytax.1e
@@ -0,0 +1,77 @@
+'\" t
+.\"     Title: ENTRYTAX
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "ENTRYTAX" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+entrytax \- Identify and retrieve sequence entries containing taxonomy IDs
+.SH "SYNOPSIS"
+.HP \w'\fBentrytax\fR\ 'u
+\fBentrytax\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-ids\ \fR\fB\fIstring\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR
+.HP \w'\fBentrytax\fR\ 'u
+\fBentrytax\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBentrytax\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqall\fR
+.RS 4
+.RE
+.PP
+\fB\-ids\fR \fIstring\fR
+.RS 4
+.RE
+.SS "Required section"
+.SS "Additional section"
+.SS "Advanced section"
+.SS "Output section"
+.PP
+\fB\-outseq\fR \fIseqoutall\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+entrytax is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/origsplitter.1e
+++ emboss-6.4.0/debian/manpages/origsplitter.1e
@@ -0,0 +1,86 @@
+'\" t
+.\"     Title: ORIGSPLITTER
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "ORIGSPLITTER" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+origsplitter \- Split a sequence into (overlapping) smaller sequences
+.SH "SYNOPSIS"
+.HP \w'\fBorigsplitter\fR\ 'u
+\fBorigsplitter\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR [\fB\-size\ \fR\fB\fIinteger\fR\fR] [\fB\-overlap\ \fR\fB\fIinteger\fR\fR] \fB\-addoverlap\ \fR\fB\fIboolean\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR
+.HP \w'\fBorigsplitter\fR\ 'u
+\fBorigsplitter\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBorigsplitter\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqall\fR
+.RS 4
+.RE
+.SS "Additional section"
+.PP
+\fB\-size\fR \fIinteger\fR
+.RS 4
+Default value: 10000
+.RE
+.PP
+\fB\-overlap\fR \fIinteger\fR
+.RS 4
+.RE
+.SS "Advanced section"
+.PP
+\fB\-addoverlap\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.SS "Output section"
+.PP
+\fB\-outseq\fR \fIseqoutall\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+origsplitter is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/rebaseextract.1e
+++ emboss-6.4.0/debian/manpages/rebaseextract.1e
@@ -0,0 +1,74 @@
+'\" t
+.\"     Title: REBASEEXTRACT
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "REBASEEXTRACT" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+rebaseextract \- Process the REBASE database for use by restriction enzyme applications
+.SH "SYNOPSIS"
+.HP \w'\fBrebaseextract\fR\ 'u
+\fBrebaseextract\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR \fB\-protofile\ \fR\fB\fIinfile\fR\fR [\fB\-equivalences\ \fR\fB\fIboolean\fR\fR]
+.HP \w'\fBrebaseextract\fR\ 'u
+\fBrebaseextract\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBrebaseextract\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Database creation" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-infile\fR \fIinfile\fR
+.RS 4
+.RE
+.PP
+\fB\-protofile\fR \fIinfile\fR
+.RS 4
+.RE
+.PP
+\fB\-equivalences\fR \fIboolean\fR
+.RS 4
+This option calculates an embossre\&.equ file using restriction enzyme prototypes in the withrefm file\&. Default value: Y
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+rebaseextract is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/dbfetchtest.1e
+++ emboss-6.4.0/debian/manpages/dbfetchtest.1e
@@ -0,0 +1,77 @@
+'\" t
+.\"     Title: DBFETCHTEST
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "DBFETCHTEST" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+dbfetchtest \- Generates server cache file for WSDbfetch data sources
+.SH "SYNOPSIS"
+.HP \w'\fBdbfetchtest\fR\ 'u
+\fBdbfetchtest\fR \fB\-servername\ \fR\fB\fIstring\fR\fR [\fB\-runtestqueries\ \fR\fB\fIboolean\fR\fR] [\fB\-outfile\ \fR\fB\fIoutfile\fR\fR]
+.HP \w'\fBdbfetchtest\fR\ 'u
+\fBdbfetchtest\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBdbfetchtest\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Display,Information" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-servername\fR \fIstring\fR
+.RS 4
+Default value: dbfetch
+.RE
+.PP
+\fB\-runtestqueries\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+Default value: stdout
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+dbfetchtest is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/trimseq.1e
+++ emboss-6.4.0/debian/manpages/trimseq.1e
@@ -0,0 +1,102 @@
+'\" t
+.\"     Title: TRIMSEQ
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "TRIMSEQ" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+trimseq \- Remove unwanted characters from start and end of sequence(s)
+.SH "SYNOPSIS"
+.HP \w'\fBtrimseq\fR\ 'u
+\fBtrimseq\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR [\fB\-window\ \fR\fB\fIinteger\fR\fR] [\fB\-percent\ \fR\fB\fIfloat\fR\fR] [\fB\-strict\ \fR\fB\fIboolean\fR\fR] [\fB\-star\ \fR\fB\fIboolean\fR\fR] \fB\-left\ \fR\fB\fIboolean\fR\fR \fB\-right\ \fR\fB\fIboolean\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR
+.HP \w'\fBtrimseq\fR\ 'u
+\fBtrimseq\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBtrimseq\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqall\fR
+.RS 4
+.RE
+.SS "Additional section"
+.PP
+\fB\-window\fR \fIinteger\fR
+.RS 4
+This determines the size of the region that is considered when deciding whether the percentage of ambiguity is greater than the threshold\&. A value of 5 means that a region of 5 letters in the sequence is shifted along the sequence from the ends and trimming is done only if there is a greater or equal percentage of ambiguity than the threshold percentage\&. Default value: 1
+.RE
+.PP
+\fB\-percent\fR \fIfloat\fR
+.RS 4
+This is the threshold of the percentage ambiguity in the window required in order to trim a sequence\&. Default value: 100\&.0
+.RE
+.PP
+\fB\-strict\fR \fIboolean\fR
+.RS 4
+In nucleic sequences, trim off not only N\*(Aqs and X\*(Aqs, but also the nucleotide IUPAC ambiguity codes M, R, W, S, Y, K, V, H, D and B\&. In protein sequences, trim off not only X\*(Aqs but also B and Z\&. Default value: N
+.RE
+.PP
+\fB\-star\fR \fIboolean\fR
+.RS 4
+In protein sequences, trim off not only X\*(Aqs, but also the *\*(Aqs Default value: N
+.RE
+.SS "Advanced section"
+.PP
+\fB\-left\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-right\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.SS "Output section"
+.PP
+\fB\-outseq\fR \fIseqoutall\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+trimseq is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/dbxstat.1e
+++ emboss-6.4.0/debian/manpages/dbxstat.1e
@@ -0,0 +1,90 @@
+'\" t
+.\"     Title: DBXSTAT
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "DBXSTAT" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+dbxstat \- Dump statistics for dbx databases
+.SH "SYNOPSIS"
+.HP \w'\fBdbxstat\fR\ 'u
+\fBdbxstat\fR \fB\-dbname\ \fR\fB\fIstring\fR\fR \fB\-field\ \fR\fB\fIstring\fR\fR \fB\-indexdir\ \fR\fB\fIdirectory\fR\fR \fB\-minimum\ \fR\fB\fIinteger\fR\fR \fB\-maximum\ \fR\fB\fIinteger\fR\fR \fB\-$(dbname)\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBdbxstat\fR\ 'u
+\fBdbxstat\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBdbxstat\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Database indexing" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-dbname\fR \fIstring\fR
+.RS 4
+.RE
+.PP
+\fB\-field\fR \fIstring\fR
+.RS 4
+Default value: id
+.RE
+.PP
+\fB\-indexdir\fR \fIdirectory\fR
+.RS 4
+.RE
+.SS "Required section"
+.SS "Advanced section"
+.PP
+\fB\-minimum\fR \fIinteger\fR
+.RS 4
+Default value: 1
+.RE
+.PP
+\fB\-maximum\fR \fIinteger\fR
+.RS 4
+.RE
+.SS "Output section"
+.PP
+\fB\-$(dbname)\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+dbxstat is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/einverted.1e
+++ emboss-6.4.0/debian/manpages/einverted.1e
@@ -0,0 +1,102 @@
+'\" t
+.\"     Title: EINVERTED
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "EINVERTED" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+einverted \- Finds inverted repeats in nucleotide sequences
+.SH "SYNOPSIS"
+.HP \w'\fBeinverted\fR\ 'u
+\fBeinverted\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-gap\ \fR\fB\fIinteger\fR\fR \fB\-threshold\ \fR\fB\fIinteger\fR\fR \fB\-match\ \fR\fB\fIinteger\fR\fR \fB\-mismatch\ \fR\fB\fIinteger\fR\fR [\fB\-maxrepeat\ \fR\fB\fIinteger\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR \fB\-outseq\ \fR\fB\fIseqout\fR\fR
+.HP \w'\fBeinverted\fR\ 'u
+\fBeinverted\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBeinverted\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Repeats,Nucleic:2D structure" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqall\fR
+.RS 4
+.RE
+.SS "Required section"
+.PP
+\fB\-gap\fR \fIinteger\fR
+.RS 4
+Default value: 12
+.RE
+.PP
+\fB\-threshold\fR \fIinteger\fR
+.RS 4
+Default value: 50
+.RE
+.PP
+\fB\-match\fR \fIinteger\fR
+.RS 4
+Default value: 3
+.RE
+.PP
+\fB\-mismatch\fR \fIinteger\fR
+.RS 4
+Default value: \-4
+.RE
+.SS "Additional section"
+.PP
+\fB\-maxrepeat\fR \fIinteger\fR
+.RS 4
+Maximum separation between the start of repeat and the end of the inverted repeat\&. Default value: 2000
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.PP
+\fB\-outseq\fR \fIseqout\fR
+.RS 4
+The sequence of the inverted repeat regions without gap characters\&.
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+einverted is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/drfindid.1e
+++ emboss-6.4.0/debian/manpages/drfindid.1e
@@ -0,0 +1,82 @@
+'\" t
+.\"     Title: DRFINDID
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "DRFINDID" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+drfindid \- Find public databases by identifier
+.SH "SYNOPSIS"
+.HP \w'\fBdrfindid\fR\ 'u
+\fBdrfindid\fR \fB\-query\ \fR\fB\fIstring\fR\fR \fB\-sensitive\ \fR\fB\fIboolean\fR\fR \fB\-subclasses\ \fR\fB\fIboolean\fR\fR \fB\-drfindid\ \fR\fB\fIoutresource\fR\fR
+.HP \w'\fBdrfindid\fR\ 'u
+\fBdrfindid\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBdrfindid\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Ontology:EDAM,Data retrieval:Resource data" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-query\fR \fIstring\fR
+.RS 4
+.RE
+.SS "Additional section"
+.SS "Advanced section"
+.PP
+\fB\-sensitive\fR \fIboolean\fR
+.RS 4
+By default, the query keywords are matched against the EDAM term names (and synonyms) only\&. This option also matches the keywords against the EDAM term definitions and will therefore (typically) report more matches\&. Default value: N
+.RE
+.PP
+\fB\-subclasses\fR \fIboolean\fR
+.RS 4
+Extend the query matches to include all terms which are specialisations (EDAM sub\-classes) of the matched type\&. Default value: Y
+.RE
+.SS "Output section"
+.PP
+\fB\-drfindid\fR \fIoutresource\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+drfindid is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/jaspextract.1e
+++ emboss-6.4.0/debian/manpages/jaspextract.1e
@@ -0,0 +1,66 @@
+'\" t
+.\"     Title: JASPEXTRACT
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "JASPEXTRACT" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+jaspextract \- Extract data from JASPAR
+.SH "SYNOPSIS"
+.HP \w'\fBjaspextract\fR\ 'u
+\fBjaspextract\fR \fB\-directory\ \fR\fB\fIdirectory\fR\fR
+.HP \w'\fBjaspextract\fR\ 'u
+\fBjaspextract\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBjaspextract\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Database creation" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-directory\fR \fIdirectory\fR
+.RS 4
+The FlatFileDir directory containing the \&.pfm files and the matrix_list\&.txt file
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+jaspextract is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/splitter.1e
+++ emboss-6.4.0/debian/manpages/splitter.1e
@@ -0,0 +1,91 @@
+'\" t
+.\"     Title: SPLITTER
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "SPLITTER" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+splitter \- Split sequence(s) into smaller sequences
+.SH "SYNOPSIS"
+.HP \w'\fBsplitter\fR\ 'u
+\fBsplitter\fR \fB\-feature\ \fR\fB\fIboolean\fR\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR [\fB\-size\ \fR\fB\fIinteger\fR\fR] [\fB\-overlap\ \fR\fB\fIinteger\fR\fR] \fB\-addoverlap\ \fR\fB\fIboolean\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR
+.HP \w'\fBsplitter\fR\ 'u
+\fBsplitter\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBsplitter\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-feature\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-sequence\fR \fIseqall\fR
+.RS 4
+.RE
+.SS "Additional section"
+.PP
+\fB\-size\fR \fIinteger\fR
+.RS 4
+Default value: 10000
+.RE
+.PP
+\fB\-overlap\fR \fIinteger\fR
+.RS 4
+.RE
+.SS "Advanced section"
+.PP
+\fB\-addoverlap\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.SS "Output section"
+.PP
+\fB\-outseq\fR \fIseqoutall\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+splitter is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/freak.1e
+++ emboss-6.4.0/debian/manpages/freak.1e
@@ -0,0 +1,96 @@
+'\" t
+.\"     Title: FREAK
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "FREAK" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+freak \- Generate residue/base frequency table or plot
+.SH "SYNOPSIS"
+.HP \w'\fBfreak\fR\ 'u
+\fBfreak\fR \fB\-seqall\ \fR\fB\fIseqall\fR\fR \fB\-letters\ \fR\fB\fIstring\fR\fR [\fB\-step\ \fR\fB\fIinteger\fR\fR] [\fB\-window\ \fR\fB\fIinteger\fR\fR] \fB\-plot\ \fR\fB\fItoggle\fR\fR \fB\-graph\ \fR\fB\fIxygraph\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBfreak\fR\ 'u
+\fBfreak\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBfreak\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Composition,Protein:Composition" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-seqall\fR \fIseqall\fR
+.RS 4
+.RE
+.SS "Required section"
+.PP
+\fB\-letters\fR \fIstring\fR
+.RS 4
+Default value: gc
+.RE
+.SS "Additional section"
+.PP
+\fB\-step\fR \fIinteger\fR
+.RS 4
+Default value: 1
+.RE
+.PP
+\fB\-window\fR \fIinteger\fR
+.RS 4
+Default value: 30
+.RE
+.SS "Output section"
+.PP
+\fB\-plot\fR \fItoggle\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-graph\fR \fIxygraph\fR
+.RS 4
+.RE
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+freak is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/fuzzpro.1e
+++ emboss-6.4.0/debian/manpages/fuzzpro.1e
@@ -0,0 +1,75 @@
+'\" t
+.\"     Title: FUZZPRO
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "FUZZPRO" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+fuzzpro \- Search for patterns in protein sequences
+.SH "SYNOPSIS"
+.HP \w'\fBfuzzpro\fR\ 'u
+\fBfuzzpro\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-pattern\ \fR\fB\fIpattern\fR\fR \fB\-outfile\ \fR\fB\fIreport\fR\fR
+.HP \w'\fBfuzzpro\fR\ 'u
+\fBfuzzpro\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBfuzzpro\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Protein:Motifs" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqall\fR
+.RS 4
+.RE
+.PP
+\fB\-pattern\fR \fIpattern\fR
+.RS 4
+The standard IUPAC one\-letter codes for the amino acids are used\&. The symbol \*(Aqx\*(Aq is used for a position where any amino acid is accepted\&. Ambiguities are indicated by listing the acceptable amino acids for a given position, between square parentheses \*(Aq[ ]\*(Aq\&. For example: [ALT] stands for Ala or Leu or Thr\&. Ambiguities are also indicated by listing between a pair of curly brackets \*(Aq{ }\*(Aq the amino acids that are not accepted at a given position\&. For example: {AM} stands for any amino acid except Ala and Met\&. Each element in a pattern is separated from its neighbor by a \*(Aq\-\*(Aq\&. (Optional in fuzzpro)\&. Repetition of an element of the pattern can be indicated by following that element with a numerical value or a numerical range between parenthesis\&. Examples: x(3) corresponds to x\-x\-x, x(2,4) corresponds to x\-x or x\-x\-x or x\-x\-x\-x\&. When a pattern is restricted to either the N\- or C\-terminal of a sequence, that pattern either starts with a \*(Aq<\*(Aq symbol or respectively ends with a \*(Aq>\*(Aq symbol\&. A period ends the pattern\&. (Optional in fuzzpro)\&. For example, [DE](2)HS{P}X(2)PX(2,4)C
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIreport\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+fuzzpro is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/oddcomp.1e
+++ emboss-6.4.0/debian/manpages/oddcomp.1e
@@ -0,0 +1,93 @@
+'\" t
+.\"     Title: ODDCOMP
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "ODDCOMP" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+oddcomp \- Identify proteins with specified sequence word composition
+.SH "SYNOPSIS"
+.HP \w'\fBoddcomp\fR\ 'u
+\fBoddcomp\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR \fB\-fullwindow\ \fR\fB\fItoggle\fR\fR \fB\-window\ \fR\fB\fIinteger\fR\fR \fB\-ignorebz\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBoddcomp\fR\ 'u
+\fBoddcomp\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBoddcomp\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Protein:Composition" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqall\fR
+.RS 4
+.RE
+.PP
+\fB\-infile\fR \fIinfile\fR
+.RS 4
+This is a file in the format of the output produced by \*(Aqcompseq\*(Aq that is used to set the minimum frequencies of words in this analysis\&.
+.RE
+.SS "Required section"
+.PP
+\fB\-fullwindow\fR \fItoggle\fR
+.RS 4
+Set this option on (Y) if you want the window size to be set to the length of the current protein\&. Otherwise, leave this option unset, in which case you\*(Aqll be prompted for a window size to use\&. Default value: N
+.RE
+.PP
+\fB\-window\fR \fIinteger\fR
+.RS 4
+This is the size of window in which to count\&. Thus if you want to count frequencies in a 40 aa stretch you should enter 40 here\&. Default value: 30
+.RE
+.SS "Advanced section"
+.PP
+\fB\-ignorebz\fR \fIboolean\fR
+.RS 4
+The amino acid code B represents Asparagine or Aspartic acid and the code Z represents Glutamine or Glutamic acid\&. These are not commonly used codes and you may wish not to count words containing them, just noting them in the count of \*(AqOther\*(Aq words\&. Default value: Y
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+This is the results file\&.
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+oddcomp is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/palindrome.1e
+++ emboss-6.4.0/debian/manpages/palindrome.1e
@@ -0,0 +1,95 @@
+'\" t
+.\"     Title: PALINDROME
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "PALINDROME" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+palindrome \- Finds inverted repeats in nucleotide sequence(s)
+.SH "SYNOPSIS"
+.HP \w'\fBpalindrome\fR\ 'u
+\fBpalindrome\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-minpallen\ \fR\fB\fIinteger\fR\fR \fB\-maxpallen\ \fR\fB\fIinteger\fR\fR \fB\-gaplimit\ \fR\fB\fIinteger\fR\fR \fB\-nummismatches\ \fR\fB\fIinteger\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR \fB\-overlap\ \fR\fB\fIboolean\fR\fR
+.HP \w'\fBpalindrome\fR\ 'u
+\fBpalindrome\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBpalindrome\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Repeats" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqall\fR
+.RS 4
+.RE
+.SS "Required section"
+.PP
+\fB\-minpallen\fR \fIinteger\fR
+.RS 4
+Default value: 10
+.RE
+.PP
+\fB\-maxpallen\fR \fIinteger\fR
+.RS 4
+Default value: 100
+.RE
+.PP
+\fB\-gaplimit\fR \fIinteger\fR
+.RS 4
+Default value: 100
+.RE
+.PP
+\fB\-nummismatches\fR \fIinteger\fR
+.RS 4
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.PP
+\fB\-overlap\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+palindrome is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/remap.1e
+++ emboss-6.4.0/debian/manpages/remap.1e
@@ -0,0 +1,225 @@
+'\" t
+.\"     Title: REMAP
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "REMAP" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+remap \- Display restriction enzyme binding sites in a nucleotide sequence
+.SH "SYNOPSIS"
+.HP \w'\fBremap\fR\ 'u
+\fBremap\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-mfile\ \fR\fB\fIdatafile\fR\fR \fB\-enzymes\ \fR\fB\fIstring\fR\fR \fB\-sitelen\ \fR\fB\fIinteger\fR\fR [\fB\-mincuts\ \fR\fB\fIinteger\fR\fR] [\fB\-maxcuts\ \fR\fB\fIinteger\fR\fR] [\fB\-single\ \fR\fB\fIboolean\fR\fR] [\fB\-blunt\ \fR\fB\fIboolean\fR\fR] [\fB\-sticky\ \fR\fB\fIboolean\fR\fR] [\fB\-ambiguity\ \fR\fB\fIboolean\fR\fR] [\fB\-plasmid\ \fR\fB\fIboolean\fR\fR] [\fB\-methylation\ \fR\fB\fIboolean\fR\fR] [\fB\-commercial\ \fR\fB\fIboolean\fR\fR] [\fB\-table\ \fR\fB\fIlist\fR\fR] [\fB\-frame\ \fR\fB\fIlist\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-cutlist\ \fR\fB\fIboolean\fR\fR] [\fB\-flatreformat\ \fR\fB\fIboolean\fR\fR] [\fB\-limit\ \fR\fB\fIboolean\fR\fR] \fB\-translation\ \fR\fB\fIboolean\fR\fR \fB\-reverse\ \fR\fB\fIboolean\fR\fR \fB\-orfminsize\ \fR\fB\fIinteger\fR\fR \fB\-uppercase\ \fR\fB\fIrange\fR\fR \fB\-highlight\ \fR\fB\fIrange\fR\fR \fB\-threeletter\ \fR\fB\fIboolean\fR\fR \fB\-number\ \fR\fB\fIboolean\fR\fR \fB\-width\ \fR\fB\fIinteger\fR\fR \fB\-length\ \fR\fB\fIinteger\fR\fR \fB\-margin\ \fR\fB\fIinteger\fR\fR \fB\-name\ \fR\fB\fIboolean\fR\fR \fB\-description\ \fR\fB\fIboolean\fR\fR \fB\-offset\ \fR\fB\fIinteger\fR\fR \fB\-html\ \fR\fB\fIboolean\fR\fR
+.HP \w'\fBremap\fR\ 'u
+\fBremap\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBremap\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Display,Nucleic:Restriction,Nucleic:Translation" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqall\fR
+.RS 4
+.RE
+.PP
+\fB\-mfile\fR \fIdatafile\fR
+.RS 4
+Default value: Emethylsites\&.dat
+.RE
+.SS "Required section"
+.PP
+\fB\-enzymes\fR \fIstring\fR
+.RS 4
+The name \*(Aqall\*(Aq reads in all enzyme names from the REBASE database\&. You can specify enzymes by giving their names with commas between then, such as: \*(AqHincII,hinfI,ppiI,hindiii\*(Aq\&. The case of the names is not important\&. You can specify a file of enzyme names to read in by giving the name of the file holding the enzyme names with a \*(Aq@\*(Aq character in front of it, for example, \*(Aq@enz\&.list\*(Aq\&. Blank lines and lines starting with a hash character or \*(Aq!\*(Aq are ignored and all other lines are concatenated together with a comma character \*(Aq,\*(Aq and then treated as the list of enzymes to search for\&. An example of a file of enzyme names is: ! my enzymes HincII, ppiII ! other enzymes hindiii HinfI PpiI Default value: all
+.RE
+.PP
+\fB\-sitelen\fR \fIinteger\fR
+.RS 4
+This sets the minimum length of the restriction enzyme recognition site\&. Any enzymes with sites shorter than this will be ignored\&. Default value: 4
+.RE
+.SS "Additional section"
+.PP
+\fB\-mincuts\fR \fIinteger\fR
+.RS 4
+This sets the minimum number of cuts for any restriction enzyme that will be considered\&. Any enzymes that cut fewer times than this will be ignored\&. Default value: 1
+.RE
+.PP
+\fB\-maxcuts\fR \fIinteger\fR
+.RS 4
+This sets the maximum number of cuts for any restriction enzyme that will be considered\&. Any enzymes that cut more times than this will be ignored\&. Default value: 2000000000
+.RE
+.PP
+\fB\-single\fR \fIboolean\fR
+.RS 4
+If this is set then this forces the values of the mincuts and maxcuts qualifiers to both be 1\&. Any other value you may have set them to will be ignored\&. Default value: N
+.RE
+.PP
+\fB\-blunt\fR \fIboolean\fR
+.RS 4
+This allows those enzymes which cut at the same position on the forward and reverse strands to be considered\&. Default value: Y
+.RE
+.PP
+\fB\-sticky\fR \fIboolean\fR
+.RS 4
+This allows those enzymes which cut at different positions on the forward and reverse strands, leaving an overhang, to be considered\&. Default value: Y
+.RE
+.PP
+\fB\-ambiguity\fR \fIboolean\fR
+.RS 4
+This allows those enzymes which have one or more \*(AqN\*(Aq ambiguity codes in their pattern to be considered Default value: Y
+.RE
+.PP
+\fB\-plasmid\fR \fIboolean\fR
+.RS 4
+If this is set then this allows searches for restriction enzyme recognition site and cut positions that span the end of the sequence to be considered\&. Default value: N
+.RE
+.PP
+\fB\-methylation\fR \fIboolean\fR
+.RS 4
+If this is set then RE recognition sites will not match methylated bases\&. Default value: N
+.RE
+.PP
+\fB\-commercial\fR \fIboolean\fR
+.RS 4
+If this is set, then only those enzymes with a commercial supplier will be searched for\&. This qualifier is ignored if you have specified an explicit list of enzymes to search for, rather than searching through \*(Aqall\*(Aq the enzymes in the REBASE database\&. It is assumed that, if you are asking for an explicit enzyme, then you probably know where to get it from and so all enzymes names that you have asked to be searched for, and which cut, will be reported whether or not they have a commercial supplier\&. Default value: Y
+.RE
+.PP
+\fB\-table\fR \fIlist\fR
+.RS 4
+.RE
+.PP
+\fB\-frame\fR \fIlist\fR
+.RS 4
+This allows you to specify the frames that are translated\&. If you are not displaying cut sites on the reverse sense, then the reverse sense translations will not be displayed even if you have requested frames 4, 5 or 6\&. By default, all six frames will be displayed\&. Default value: 6
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.PP
+\fB\-cutlist\fR \fIboolean\fR
+.RS 4
+This produces lists in the output of the enzymes that cut, those that cut but are excluded because that cut fewer times than mincut or more times than maxcut and those enzymes that do not cut\&. Default value: Y
+.RE
+.PP
+\fB\-flatreformat\fR \fIboolean\fR
+.RS 4
+This changes the output format to one where the recognition site is indicated by a row of \*(Aq===\*(Aq characters and the cut site is pointed to by a \*(Aq>\*(Aq character in the forward sense, or a \*(Aq<\*(Aq in the reverse sense strand\&. Default value: N
+.RE
+.PP
+\fB\-limit\fR \fIboolean\fR
+.RS 4
+This limits the reporting of enzymes to just one enzyme from each group of isoschizomers\&. The enzyme chosen to represent an isoschizomer group is the prototype indicated in the data file \*(Aqembossre\&.equ\*(Aq, which is created by the program \*(Aqrebaseextract\*(Aq\&. If you prefer different prototypes to be used, make a copy of embossre\&.equ in your home directory and edit it\&. If this value is set to be false then all of the input enzymes will be reported\&. You might like to set this to false if you are supplying an explicit set of enzymes rather than searching \*(Aqall\*(Aq of them\&. Default value: Y
+.RE
+.PP
+\fB\-translation\fR \fIboolean\fR
+.RS 4
+This displays the 6\-frame translations of the sequence in the output\&. Default value: Y
+.RE
+.PP
+\fB\-reverse\fR \fIboolean\fR
+.RS 4
+This displays the cut sites and translation of the reverse sense\&. Default value: Y
+.RE
+.PP
+\fB\-orfminsize\fR \fIinteger\fR
+.RS 4
+This sets the minimum size of Open Reading Frames (ORFs) to display in the translations\&. All other translation regions are masked by changing the amino acids to \*(Aq\-\*(Aq characters\&.
+.RE
+.PP
+\fB\-uppercase\fR \fIrange\fR
+.RS 4
+Regions to put in uppercase\&. If this is left blank, then the sequence case is left alone\&. A set of regions is specified by a set of pairs of positions\&. The positions are integers\&. They are separated by any non\-digit, non\-alpha character\&. Examples of region specifications are: 24\-45, 56\-78 1:45, 67=99;765\&.\&.888 1,5,8,10,23,45,57,99
+.RE
+.PP
+\fB\-highlight\fR \fIrange\fR
+.RS 4
+Regions to colour if formatting for HTML\&. If this is left blank, then the sequence is left alone\&. A set of regions is specified by a set of pairs of positions\&. The positions are integers\&. They are followed by any valid HTML font colour\&. Examples of region specifications are: 24\-45 blue 56\-78 orange 1\-100 green 120\-156 red A file of ranges to colour (one range per line) can be specified as \*(Aq@filename\*(Aq\&.
+.RE
+.PP
+\fB\-threeletter\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-number\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-width\fR \fIinteger\fR
+.RS 4
+Default value: 60
+.RE
+.PP
+\fB\-length\fR \fIinteger\fR
+.RS 4
+.RE
+.PP
+\fB\-margin\fR \fIinteger\fR
+.RS 4
+Default value: 10
+.RE
+.PP
+\fB\-name\fR \fIboolean\fR
+.RS 4
+Set this to be false if you do not wish to display the ID name of the sequence Default value: Y
+.RE
+.PP
+\fB\-description\fR \fIboolean\fR
+.RS 4
+Set this to be false if you do not wish to display the description of the sequence Default value: Y
+.RE
+.PP
+\fB\-offset\fR \fIinteger\fR
+.RS 4
+Default value: 1
+.RE
+.PP
+\fB\-html\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+remap is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/pasteseq.1e
+++ emboss-6.4.0/debian/manpages/pasteseq.1e
@@ -0,0 +1,80 @@
+'\" t
+.\"     Title: PASTESEQ
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "PASTESEQ" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+pasteseq \- Insert one sequence into another
+.SH "SYNOPSIS"
+.HP \w'\fBpasteseq\fR\ 'u
+\fBpasteseq\fR \fB\-asequence\ \fR\fB\fIsequence\fR\fR \fB\-bsequence\ \fR\fB\fIsequence\fR\fR \fB\-pos\ \fR\fB\fIinteger\fR\fR \fB\-outseq\ \fR\fB\fIseqout\fR\fR
+.HP \w'\fBpasteseq\fR\ 'u
+\fBpasteseq\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBpasteseq\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-asequence\fR \fIsequence\fR
+.RS 4
+.RE
+.PP
+\fB\-bsequence\fR \fIsequence\fR
+.RS 4
+.RE
+.SS "Required section"
+.PP
+\fB\-pos\fR \fIinteger\fR
+.RS 4
+The position in the main input sequence to insert after\&. To insert before the start use the position 0\&. Default value: $(asequence\&.end)
+.RE
+.SS "Output section"
+.PP
+\fB\-outseq\fR \fIseqout\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+pasteseq is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/dbxtax.1e
+++ emboss-6.4.0/debian/manpages/dbxtax.1e
@@ -0,0 +1,108 @@
+'\" t
+.\"     Title: DBXTAX
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "DBXTAX" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+dbxtax \- Index NCBI taxonomy using b+tree indices
+.SH "SYNOPSIS"
+.HP \w'\fBdbxtax\fR\ 'u
+\fBdbxtax\fR \fB\-dbname\ \fR\fB\fIstring\fR\fR \fB\-dbresource\ \fR\fB\fIstring\fR\fR \fB\-directory\ \fR\fB\fIdirectory\fR\fR \fB\-fields\ \fR\fB\fIlist\fR\fR \fB\-compressed\ \fR\fB\fIboolean\fR\fR \fB\-release\ \fR\fB\fIstring\fR\fR \fB\-date\ \fR\fB\fIstring\fR\fR \fB\-indexoutdir\ \fR\fB\fIoutdir\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBdbxtax\fR\ 'u
+\fBdbxtax\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBdbxtax\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Database indexing" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-dbname\fR \fIstring\fR
+.RS 4
+Default value: taxon
+.RE
+.PP
+\fB\-dbresource\fR \fIstring\fR
+.RS 4
+Default value: taxresource
+.RE
+.PP
+\fB\-directory\fR \fIdirectory\fR
+.RS 4
+Default value: \&.
+.RE
+.SS "Required section"
+.PP
+\fB\-fields\fR \fIlist\fR
+.RS 4
+Default value: *
+.RE
+.PP
+\fB\-compressed\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.SS "Advanced section"
+.PP
+\fB\-release\fR \fIstring\fR
+.RS 4
+Default value: 0\&.0
+.RE
+.PP
+\fB\-date\fR \fIstring\fR
+.RS 4
+Default value: 00/00/00
+.RE
+.SS "Output section"
+.PP
+\fB\-indexoutdir\fR \fIoutdir\fR
+.RS 4
+Default value: \&.
+.RE
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+dbxtax is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/acdtrace.1e
+++ emboss-6.4.0/debian/manpages/acdtrace.1e
@@ -0,0 +1,65 @@
+'\" t
+.\"     Title: ACDTRACE
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "ACDTRACE" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+acdtrace \- Trace processing of an application ACD file (for testing)
+.SH "SYNOPSIS"
+.HP \w'\fBacdtrace\fR\ 'u
+\fBacdtrace\fR \fB\-program\ \fR\fB\fIstring\fR\fR
+.HP \w'\fBacdtrace\fR\ 'u
+\fBacdtrace\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBacdtrace\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Acd,Data retrieval:Tool data" command group(s)\&.
+.SH "OPTIONS"
+.SS "Required section"
+.PP
+\fB\-program\fR \fIstring\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+acdtrace is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/dbxflat.1e
+++ emboss-6.4.0/debian/manpages/dbxflat.1e
@@ -0,0 +1,125 @@
+'\" t
+.\"     Title: DBXFLAT
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "DBXFLAT" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+dbxflat \- Index a flat file database using b+tree indices
+.SH "SYNOPSIS"
+.HP \w'\fBdbxflat\fR\ 'u
+\fBdbxflat\fR \fB\-dbname\ \fR\fB\fIstring\fR\fR \fB\-dbresource\ \fR\fB\fIstring\fR\fR \fB\-idformat\ \fR\fB\fIlist\fR\fR \fB\-filenames\ \fR\fB\fIstring\fR\fR \fB\-directory\ \fR\fB\fIdirectory\fR\fR \fB\-fields\ \fR\fB\fIlist\fR\fR \fB\-compressed\ \fR\fB\fIboolean\fR\fR \fB\-release\ \fR\fB\fIstring\fR\fR \fB\-date\ \fR\fB\fIstring\fR\fR \fB\-exclude\ \fR\fB\fIstring\fR\fR \fB\-statistics\ \fR\fB\fIboolean\fR\fR \fB\-indexoutdir\ \fR\fB\fIoutdir\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBdbxflat\fR\ 'u
+\fBdbxflat\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBdbxflat\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Database indexing" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-dbname\fR \fIstring\fR
+.RS 4
+.RE
+.PP
+\fB\-dbresource\fR \fIstring\fR
+.RS 4
+.RE
+.PP
+\fB\-idformat\fR \fIlist\fR
+.RS 4
+Default value: SWISS
+.RE
+.PP
+\fB\-filenames\fR \fIstring\fR
+.RS 4
+Default value: *\&.dat
+.RE
+.PP
+\fB\-directory\fR \fIdirectory\fR
+.RS 4
+Default value: \&.
+.RE
+.SS "Required section"
+.PP
+\fB\-fields\fR \fIlist\fR
+.RS 4
+Default value: id,acc
+.RE
+.PP
+\fB\-compressed\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.SS "Advanced section"
+.PP
+\fB\-release\fR \fIstring\fR
+.RS 4
+Default value: 0\&.0
+.RE
+.PP
+\fB\-date\fR \fIstring\fR
+.RS 4
+Default value: 00/00/00
+.RE
+.PP
+\fB\-exclude\fR \fIstring\fR
+.RS 4
+.RE
+.PP
+\fB\-statistics\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.SS "Output section"
+.PP
+\fB\-indexoutdir\fR \fIoutdir\fR
+.RS 4
+Default value: \&.
+.RE
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+dbxflat is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/pepwheel.1e
+++ emboss-6.4.0/debian/manpages/pepwheel.1e
@@ -0,0 +1,106 @@
+'\" t
+.\"     Title: PEPWHEEL
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "PEPWHEEL" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+pepwheel \- Draw a helical wheel diagram for a protein sequence
+.SH "SYNOPSIS"
+.HP \w'\fBpepwheel\fR\ 'u
+\fBpepwheel\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR \fB\-wheel\ \fR\fB\fIboolean\fR\fR [\fB\-steps\ \fR\fB\fIinteger\fR\fR] [\fB\-turns\ \fR\fB\fIinteger\fR\fR] \fB\-graph\ \fR\fB\fIgraph\fR\fR \fB\-amphipathic\ \fR\fB\fItoggle\fR\fR \fB\-squares\ \fR\fB\fIstring\fR\fR \fB\-diamonds\ \fR\fB\fIstring\fR\fR \fB\-octags\ \fR\fB\fIstring\fR\fR
+.HP \w'\fBpepwheel\fR\ 'u
+\fBpepwheel\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBpepwheel\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Display,Protein:2D Structure" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIsequence\fR
+.RS 4
+.RE
+.SS "Output section"
+.PP
+\fB\-wheel\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-steps\fR \fIinteger\fR
+.RS 4
+The number of residues plotted per turn is this value divided by the \*(Aqturns\*(Aq value\&. Default value: 18
+.RE
+.PP
+\fB\-turns\fR \fIinteger\fR
+.RS 4
+The number of residues plotted per turn is the \*(Aqsteps\*(Aq value divided by this value\&. Default value: 5
+.RE
+.PP
+\fB\-graph\fR \fIgraph\fR
+.RS 4
+.RE
+.SS "Markup section"
+.PP
+\fB\-amphipathic\fR \fItoggle\fR
+.RS 4
+If this is true then the residues ACFGILMVWY are marked as squares and all other residues are unmarked\&. This overrides any other markup that you may have specified using the qualifiers \*(Aq\-squares\*(Aq, \*(Aq\-diamonds\*(Aq and \*(Aq\-octags\*(Aq\&.
+.RE
+.PP
+\fB\-squares\fR \fIstring\fR
+.RS 4
+By default the aliphatic residues ILVM are marked with squares\&. Default value: ILVM
+.RE
+.PP
+\fB\-diamonds\fR \fIstring\fR
+.RS 4
+By default the residues DENQST are marked with diamonds\&. Default value: DENQST
+.RE
+.PP
+\fB\-octags\fR \fIstring\fR
+.RS 4
+By default the positively charged residues HKR are marked with octagons\&. Default value: HKR
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+pepwheel is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/jaspscan.1e
+++ emboss-6.4.0/debian/manpages/jaspscan.1e
@@ -0,0 +1,97 @@
+'\" t
+.\"     Title: JASPSCAN
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "JASPSCAN" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+jaspscan \- Scans DNA sequences for transcription factors
+.SH "SYNOPSIS"
+.HP \w'\fBjaspscan\fR\ 'u
+\fBjaspscan\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-menu\ \fR\fB\fIlist\fR\fR \fB\-matrices\ \fR\fB\fIstring\fR\fR \fB\-threshold\ \fR\fB\fIfloat\fR\fR [\fB\-exclude\ \fR\fB\fIstring\fR\fR] [\fB\-both\ \fR\fB\fIboolean\fR\fR] \fB\-outfile\ \fR\fB\fIreport\fR\fR
+.HP \w'\fBjaspscan\fR\ 'u
+\fBjaspscan\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBjaspscan\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Transcription" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqall\fR
+.RS 4
+.RE
+.PP
+\fB\-menu\fR \fIlist\fR
+.RS 4
+Default value: C
+.RE
+.PP
+\fB\-matrices\fR \fIstring\fR
+.RS 4
+The name \*(Aqall\*(Aq reads in all matrix files from the selected JASPAR matrix set\&. You can specify individual matrices by giving their names with commas between then, such as: \*(Aqma0001\&.1,ma0015*\*(Aq\&. The case of the names is not important\&. You can specify a file of matrix names to read in by giving the name of the file holding the matrix names with a \*(Aq@\*(Aq character in front of it, for example, \*(Aq@matrix\&.list\*(Aq\&. Blank lines and lines starting with a hash character or \*(Aq!\*(Aq are ignored and all other lines are concatenated together with a comma character \*(Aq,\*(Aq and then treated as the list of enzymes to search for\&. An example of a file of matrix names is: ! my matrices ma0001\&.1, ma0002\&.1 ! other matrices ma0010\&.1 ma0032* ma0053\&.1 Default value: all
+.RE
+.SS "Required section"
+.PP
+\fB\-threshold\fR \fIfloat\fR
+.RS 4
+If the matrix score is greater than or equal to this percentage then a hit will be reported Default value: 80\&.0
+.RE
+.SS "Additional section"
+.PP
+\fB\-exclude\fR \fIstring\fR
+.RS 4
+The names of any matrices to exclude from the \*(Aqmatrices\*(Aq list\&. Matrices are specified in the same way as for the selection list\&.
+.RE
+.PP
+\fB\-both\fR \fIboolean\fR
+.RS 4
+If set then both the forward and reverse strands are searched Default value: N
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIreport\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+jaspscan is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/seqretsplit.1e
+++ emboss-6.4.0/debian/manpages/seqretsplit.1e
@@ -0,0 +1,79 @@
+'\" t
+.\"     Title: SEQRETSPLIT
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "SEQRETSPLIT" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+seqretsplit \- Reads sequences and writes them to individual files
+.SH "SYNOPSIS"
+.HP \w'\fBseqretsplit\fR\ 'u
+\fBseqretsplit\fR \fB\-feature\ \fR\fB\fIboolean\fR\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-firstonly\ \fR\fB\fIboolean\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR
+.HP \w'\fBseqretsplit\fR\ 'u
+\fBseqretsplit\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBseqretsplit\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-feature\fR \fIboolean\fR
+.RS 4
+.RE
+.PP
+\fB\-sequence\fR \fIseqall\fR
+.RS 4
+.RE
+.SS "Advanced section"
+.PP
+\fB\-firstonly\fR \fIboolean\fR
+.RS 4
+.RE
+.SS "Output section"
+.PP
+\fB\-outseq\fR \fIseqoutall\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+seqretsplit is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/entrygo.1e
+++ emboss-6.4.0/debian/manpages/entrygo.1e
@@ -0,0 +1,77 @@
+'\" t
+.\"     Title: ENTRYGO
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "ENTRYGO" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+entrygo \- Identify and retrieve sequence entries containing GO terms
+.SH "SYNOPSIS"
+.HP \w'\fBentrygo\fR\ 'u
+\fBentrygo\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-term\ \fR\fB\fIstring\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR
+.HP \w'\fBentrygo\fR\ 'u
+\fBentrygo\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBentrygo\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqall\fR
+.RS 4
+.RE
+.PP
+\fB\-term\fR \fIstring\fR
+.RS 4
+.RE
+.SS "Required section"
+.SS "Additional section"
+.SS "Advanced section"
+.SS "Output section"
+.PP
+\fB\-outseq\fR \fIseqoutall\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+entrygo is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/trimest.1e
+++ emboss-6.4.0/debian/manpages/trimest.1e
@@ -0,0 +1,97 @@
+'\" t
+.\"     Title: TRIMEST
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "TRIMEST" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+trimest \- Remove poly\-A tails from nucleotide sequences
+.SH "SYNOPSIS"
+.HP \w'\fBtrimest\fR\ 'u
+\fBtrimest\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR [\fB\-minlength\ \fR\fB\fIinteger\fR\fR] [\fB\-mismatches\ \fR\fB\fIinteger\fR\fR] [\fB\-reverse\ \fR\fB\fIboolean\fR\fR] [\fB\-tolower\ \fR\fB\fItoggle\fR\fR] \fB\-fiveprime\ \fR\fB\fIboolean\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR
+.HP \w'\fBtrimest\fR\ 'u
+\fBtrimest\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBtrimest\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Functional sites,Edit" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqall\fR
+.RS 4
+.RE
+.SS "Additional section"
+.PP
+\fB\-minlength\fR \fIinteger\fR
+.RS 4
+This is the minimum length that a poly\-A (or poly\-T) tail must have before it is removed\&. If there are mismatches in the tail than there must be at least this length of poly\-A tail before the mismatch for the mismatch to be considered part of the tail\&. Default value: 4
+.RE
+.PP
+\fB\-mismatches\fR \fIinteger\fR
+.RS 4
+If there are this number or fewer contiguous non\-A bases in a poly\-A tail then, if there are \*(Aq\-minlength\*(Aq \*(AqA\*(Aq bases before them, they will be considered part of the tail and removed \&. For example the terminal 4 A\*(Aqs of GCAGAAAA would be removed with the default values of \-minlength=4 and \-mismatches=1 (There are not at least 4 A\*(Aqs before the last \*(AqG\*(Aq and so only the A\*(Aqs after it are considered to be part of the tail)\&. The terminal 9 bases of GCAAAAGAAAA would be removed; There are at least \-minlength A\*(Aqs preceeding the last \*(AqG\*(Aq, so it is part of the tail\&. Default value: 1
+.RE
+.PP
+\fB\-reverse\fR \fIboolean\fR
+.RS 4
+When a poly\-T region at the 5\*(Aq end of the sequence is found and removed, it is likely that the sequence is in the reverse sense\&. This option will change the sequence to the forward sense when it is written out\&. If this option is not set, then the sense will not be changed\&. Default value: Y
+.RE
+.PP
+\fB\-tolower\fR \fItoggle\fR
+.RS 4
+The poly\-A region can be \*(Aqmasked\*(Aq by converting the sequence characters to lower\-case\&. Some non\-EMBOSS programs e\&.g\&. fasta can interpret this as a masked region\&. The sequence is unchanged apart from the case change\&. You might like to ensure that the whole sequence is in upper\-case before masking the specified regions to lower\-case by using the \*(Aq\-supper\*(Aq sequence qualifier\&. Default value: N
+.RE
+.SS "Advanced section"
+.PP
+\fB\-fiveprime\fR \fIboolean\fR
+.RS 4
+If this is set true, then the 5\*(Aq end of the sequence is inspected for poly\-T tails\&. These will be removed if they are longer than any 3\*(Aq poly\-A tails\&. If this is false, then the 5\*(Aq end is ignored\&. Default value: Y
+.RE
+.SS "Output section"
+.PP
+\fB\-outseq\fR \fIseqoutall\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+trimest is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/twofeat.1e
+++ emboss-6.4.0/debian/manpages/twofeat.1e
@@ -0,0 +1,183 @@
+'\" t
+.\"     Title: TWOFEAT
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "TWOFEAT" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+twofeat \- Finds neighbouring pairs of features in sequence(s)
+.SH "SYNOPSIS"
+.HP \w'\fBtwofeat\fR\ 'u
+\fBtwofeat\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR [\fB\-asource\ \fR\fB\fIstring\fR\fR] \fB\-atype\ \fR\fB\fIstring\fR\fR [\fB\-asense\ \fR\fB\fIlist\fR\fR] [\fB\-aminscore\ \fR\fB\fIfloat\fR\fR] [\fB\-amaxscore\ \fR\fB\fIfloat\fR\fR] [\fB\-atag\ \fR\fB\fIstring\fR\fR] [\fB\-avalue\ \fR\fB\fIstring\fR\fR] [\fB\-bsource\ \fR\fB\fIstring\fR\fR] \fB\-btype\ \fR\fB\fIstring\fR\fR [\fB\-bsense\ \fR\fB\fIlist\fR\fR] [\fB\-bminscore\ \fR\fB\fIfloat\fR\fR] [\fB\-bmaxscore\ \fR\fB\fIfloat\fR\fR] [\fB\-btag\ \fR\fB\fIstring\fR\fR] [\fB\-bvalue\ \fR\fB\fIstring\fR\fR] [\fB\-overlap\ \fR\fB\fIlist\fR\fR] \fB\-minrange\ \fR\fB\fIinteger\fR\fR \fB\-maxrange\ \fR\fB\fIinteger\fR\fR [\fB\-rangetype\ \fR\fB\fIlist\fR\fR] [\fB\-sense\ \fR\fB\fIlist\fR\fR] [\fB\-order\ \fR\fB\fIlist\fR\fR] [\fB\-twoout\ \fR\fB\fItoggle\fR\fR] \fB\-typeout\ \fR\fB\fIstring\fR\fR \fB\-outfile\ \fR\fB\fIreport\fR\fR
+.HP \w'\fBtwofeat\fR\ 'u
+\fBtwofeat\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBtwofeat\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Feature tables" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqall\fR
+.RS 4
+.RE
+.SS "First feature options"
+.PP
+\fB\-asource\fR \fIstring\fR
+.RS 4
+By default any feature source in the feature table is allowed\&. You can set this to match any feature source you wish to allow\&. The source name is usually either the name of the program that detected the feature or it is the feature table (eg: EMBL) that the feature came from\&. The source may be wildcarded by using \*(Aq*\*(Aq\&. If you wish to allow more than one source, separate their names with the character \*(Aq|\*(Aq, eg: gene* | embl Default value: *
+.RE
+.PP
+\fB\-atype\fR \fIstring\fR
+.RS 4
+By default every feature in the feature table is allowed\&. You can set this to be any feature type you wish to allow\&. See http://www\&.ebi\&.ac\&.uk/embl/WebFeat/ for a list of the EMBL feature types and see Appendix A of the Swissprot user manual in http://www\&.expasy\&.org/sprot/userman\&.html for a list of the Swissprot feature types\&. The type may be wildcarded by using \*(Aq*\*(Aq\&. If you wish to allow more than one type, separate their names with the character \*(Aq|\*(Aq, eg: *UTR | intron Default value: *
+.RE
+.PP
+\fB\-asense\fR \fIlist\fR
+.RS 4
+By default any feature sense is allowed\&. You can set this to match the required sense\&.
+.RE
+.PP
+\fB\-aminscore\fR \fIfloat\fR
+.RS 4
+If this is greater than or equal to the maximum score, then any score is allowed\&. Default value: 0\&.0
+.RE
+.PP
+\fB\-amaxscore\fR \fIfloat\fR
+.RS 4
+If this is less than or equal to the maximum score, then any score is permitted\&. Default value: 0\&.0
+.RE
+.PP
+\fB\-atag\fR \fIstring\fR
+.RS 4
+Tags are the types of extra values that a feature may have\&. For example in the EMBL feature table, a \*(AqCDS\*(Aq type of feature may have the tags \*(Aq/codon\*(Aq, \*(Aq/codon_start\*(Aq, \*(Aq/db_xref\*(Aq, \*(Aq/EC_number\*(Aq, \*(Aq/evidence\*(Aq, \*(Aq/exception\*(Aq, \*(Aq/function\*(Aq, \*(Aq/gene\*(Aq, \*(Aq/label\*(Aq, \*(Aq/map\*(Aq, \*(Aq/note\*(Aq, \*(Aq/number\*(Aq, \*(Aq/partial\*(Aq, \*(Aq/product\*(Aq, \*(Aq/protein_id\*(Aq, \*(Aq/pseudo\*(Aq, \*(Aq/standard_name\*(Aq, \*(Aq/translation\*(Aq, \*(Aq/transl_except\*(Aq, \*(Aq/transl_table\*(Aq, or \*(Aq/usedin\*(Aq\&. Some of these tags also have values, for example \*(Aq/gene\*(Aq can have the value of the gene name\&. By default any feature tag in the feature table is allowed\&. You can set this to match any feature tag you wish to allow\&. The tag may be wildcarded by using \*(Aq*\*(Aq\&. If you wish to allow more than one tag, separate their names with the character \*(Aq|\*(Aq, eg: gene | label Default value: *
+.RE
+.PP
+\fB\-avalue\fR \fIstring\fR
+.RS 4
+Tag values are the values associated with a feature tag\&. Tags are the types of extra values that a feature may have\&. For example in the EMBL feature table, a \*(AqCDS\*(Aq type of feature may have the tags \*(Aq/codon\*(Aq, \*(Aq/codon_start\*(Aq, \*(Aq/db_xref\*(Aq, \*(Aq/EC_number\*(Aq, \*(Aq/evidence\*(Aq, \*(Aq/exception\*(Aq, \*(Aq/function\*(Aq, \*(Aq/gene\*(Aq, \*(Aq/label\*(Aq, \*(Aq/map\*(Aq, \*(Aq/note\*(Aq, \*(Aq/number\*(Aq, \*(Aq/partial\*(Aq, \*(Aq/product\*(Aq, \*(Aq/protein_id\*(Aq, \*(Aq/pseudo\*(Aq, \*(Aq/standard_name\*(Aq, \*(Aq/translation\*(Aq, \*(Aq/transl_except\*(Aq, \*(Aq/transl_table\*(Aq, or \*(Aq/usedin\*(Aq\&. Only some of these tags can have values, for example \*(Aq/gene\*(Aq can have the value of the gene name\&. By default any feature tag value in the feature table is allowed\&. You can set this to match any feature tag value you wish to allow\&. The tag value may be wildcarded by using \*(Aq*\*(Aq\&. If you wish to allow more than one tag value, separate their names with the character \*(Aq|\*(Aq, eg: pax* | 10 Default value: *
+.RE
+.SS "Second feature options"
+.PP
+\fB\-bsource\fR \fIstring\fR
+.RS 4
+By default any feature source in the feature table is allowed\&. You can set this to match any feature source you wish to allow\&. The source name is usually either the name of the program that detected the feature or it is the feature table (eg: EMBL) that the feature came from\&. The source may be wildcarded by using \*(Aq*\*(Aq\&. If you wish to allow more than one source, separate their names with the character \*(Aq|\*(Aq, eg: gene* | embl Default value: *
+.RE
+.PP
+\fB\-btype\fR \fIstring\fR
+.RS 4
+By default every feature in the feature table is allowed\&. You can set this to be any feature type you wish to allow\&. See http://www\&.ebi\&.ac\&.uk/embl/WebFeat/ for a list of the EMBL feature types and see Appendix A of the Swissprot user manual in http://www\&.expasy\&.org/sprot/userman\&.html for a list of the Swissprot feature types\&. The type may be wildcarded by using \*(Aq*\*(Aq\&. If you wish to allow more than one type, separate their names with the character \*(Aq|\*(Aq, eg: *UTR | intron Default value: *
+.RE
+.PP
+\fB\-bsense\fR \fIlist\fR
+.RS 4
+By default any feature sense is allowed\&. You can set this to match the required sense\&.
+.RE
+.PP
+\fB\-bminscore\fR \fIfloat\fR
+.RS 4
+If this is greater than or equal to the maximum score, then any score is allowed\&. Default value: 0\&.0
+.RE
+.PP
+\fB\-bmaxscore\fR \fIfloat\fR
+.RS 4
+If this is less than or equal to the maximum score, then any score is permitted\&. Default value: 0\&.0
+.RE
+.PP
+\fB\-btag\fR \fIstring\fR
+.RS 4
+Tags are the types of extra values that a feature may have\&. For example in the EMBL feature table, a \*(AqCDS\*(Aq type of feature may have the tags \*(Aq/codon\*(Aq, \*(Aq/codon_start\*(Aq, \*(Aq/db_xref\*(Aq, \*(Aq/EC_number\*(Aq, \*(Aq/evidence\*(Aq, \*(Aq/exception\*(Aq, \*(Aq/function\*(Aq, \*(Aq/gene\*(Aq, \*(Aq/label\*(Aq, \*(Aq/map\*(Aq, \*(Aq/note\*(Aq, \*(Aq/number\*(Aq, \*(Aq/partial\*(Aq, \*(Aq/product\*(Aq, \*(Aq/protein_id\*(Aq, \*(Aq/pseudo\*(Aq, \*(Aq/standard_name\*(Aq, \*(Aq/translation\*(Aq, \*(Aq/transl_except\*(Aq, \*(Aq/transl_table\*(Aq, or \*(Aq/usedin\*(Aq\&. Some of these tags also have values, for example \*(Aq/gene\*(Aq can have the value of the gene name\&. By default any feature tag in the feature table is allowed\&. You can set this to match any feature tag you wish to allow\&. The tag may be wildcarded by using \*(Aq*\*(Aq\&. If you wish to allow more than one tag, separate their names with the character \*(Aq|\*(Aq, eg: gene | label Default value: *
+.RE
+.PP
+\fB\-bvalue\fR \fIstring\fR
+.RS 4
+Tag values are the values associated with a feature tag\&. Tags are the types of extra values that a feature may have\&. For example in the EMBL feature table, a \*(AqCDS\*(Aq type of feature may have the tags \*(Aq/codon\*(Aq, \*(Aq/codon_start\*(Aq, \*(Aq/db_xref\*(Aq, \*(Aq/EC_number\*(Aq, \*(Aq/evidence\*(Aq, \*(Aq/exception\*(Aq, \*(Aq/function\*(Aq, \*(Aq/gene\*(Aq, \*(Aq/label\*(Aq, \*(Aq/map\*(Aq, \*(Aq/note\*(Aq, \*(Aq/number\*(Aq, \*(Aq/partial\*(Aq, \*(Aq/product\*(Aq, \*(Aq/protein_id\*(Aq, \*(Aq/pseudo\*(Aq, \*(Aq/standard_name\*(Aq, \*(Aq/translation\*(Aq, \*(Aq/transl_except\*(Aq, \*(Aq/transl_table\*(Aq, or \*(Aq/usedin\*(Aq\&. Only some of these tags can have values, for example \*(Aq/gene\*(Aq can have the value of the gene name\&. By default any feature tag value in the feature table is allowed\&. You can set this to match any feature tag value you wish to allow\&. The tag value may be wildcarded by using \*(Aq*\*(Aq\&. If you wish to allow more than one tag value, separate their names with the character \*(Aq|\*(Aq, eg: pax* | 10 Default value: *
+.RE
+.SS "Feature relation options"
+.PP
+\fB\-overlap\fR \fIlist\fR
+.RS 4
+This allows you to specify the allowed overlaps of the features A and B\&. You can allow any or no overlaps, specify that they must or must not overlap, that one must or must not be wholly enclosed within another feature\&. Default value: A
+.RE
+.PP
+\fB\-minrange\fR \fIinteger\fR
+.RS 4
+If this is greater or equal to \*(Aqmaxrange\*(Aq, then no min or max range is specified
+.RE
+.PP
+\fB\-maxrange\fR \fIinteger\fR
+.RS 4
+If this is less than or equal to \*(Aqminrange\*(Aq, then no min or max range is specified
+.RE
+.PP
+\fB\-rangetype\fR \fIlist\fR
+.RS 4
+This allows you to specify the positions from which the allowed minimum or maximum distance between the features is measured Default value: N
+.RE
+.PP
+\fB\-sense\fR \fIlist\fR
+.RS 4
+This allows you to specify the required sense that the two features must be on\&. This is ignored (always \*(AqAny\*(Aq) when looking at protein sequence features\&. Default value: A
+.RE
+.PP
+\fB\-order\fR \fIlist\fR
+.RS 4
+This allows you to specify the required order of the two features\&. The order is measured from the start positions of the features\&. This criterion is always applied despite the specified overlap type required\&. Default value: A
+.RE
+.SS "Output section"
+.PP
+\fB\-twoout\fR \fItoggle\fR
+.RS 4
+If you set this to be true, then the two features themselves will be written out\&. If it is left as false, then a single feature will be written out covering the two features you found\&. Default value: N
+.RE
+.PP
+\fB\-typeout\fR \fIstring\fR
+.RS 4
+If you have specified that the pairs of features that are found should be reported as one feature in the ouput, then you can specify the \*(Aqtype\*(Aq name of the new feature here\&. By default every feature in the feature table is allowed\&. See http://www\&.ebi\&.ac\&.uk/embl/WebFeat/ for a list of the EMBL feature types and see Appendix A of the Swissprot user manual in http://www\&.expasy\&.org/sprot/userman\&.html for a list of the Swissprot feature types\&. If you specify an invalid feature type name, then the default name \*(Aqmisc_feature\*(Aq is used\&. Default value: misc_feature
+.RE
+.PP
+\fB\-outfile\fR \fIreport\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+twofeat is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/sqltest.1e
+++ emboss-6.4.0/debian/manpages/sqltest.1e
@@ -0,0 +1,66 @@
+'\" t
+.\"     Title: SQLTEST
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "SQLTEST" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+sqltest \- Demonstration of SQL server access
+.SH "SYNOPSIS"
+.HP \w'\fBsqltest\fR\ 'u
+\fBsqltest\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBsqltest\fR\ 'u
+\fBsqltest\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBsqltest\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Test" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+sqltest is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/dbxcompress.1e
+++ emboss-6.4.0/debian/manpages/dbxcompress.1e
@@ -0,0 +1,80 @@
+'\" t
+.\"     Title: DBXCOMPRESS
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "DBXCOMPRESS" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+dbxcompress \- Compress an uncompressed dbx index
+.SH "SYNOPSIS"
+.HP \w'\fBdbxcompress\fR\ 'u
+\fBdbxcompress\fR \fB\-dbname\ \fR\fB\fIstring\fR\fR \fB\-field\ \fR\fB\fIstring\fR\fR \fB\-indexdir\ \fR\fB\fIdirectory\fR\fR \fB\-$(dbname)\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBdbxcompress\fR\ 'u
+\fBdbxcompress\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBdbxcompress\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Database indexing" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-dbname\fR \fIstring\fR
+.RS 4
+.RE
+.PP
+\fB\-field\fR \fIstring\fR
+.RS 4
+.RE
+.PP
+\fB\-indexdir\fR \fIdirectory\fR
+.RS 4
+.RE
+.SS "Required section"
+.SS "Advanced section"
+.SS "Output section"
+.PP
+\fB\-$(dbname)\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+dbxcompress is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/patmatdb.1e
+++ emboss-6.4.0/debian/manpages/patmatdb.1e
@@ -0,0 +1,76 @@
+'\" t
+.\"     Title: PATMATDB
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "PATMATDB" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+patmatdb \- Searches protein sequences with a sequence motif
+.SH "SYNOPSIS"
+.HP \w'\fBpatmatdb\fR\ 'u
+\fBpatmatdb\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-motif\ \fR\fB\fIstring\fR\fR \fB\-outfile\ \fR\fB\fIreport\fR\fR
+.HP \w'\fBpatmatdb\fR\ 'u
+\fBpatmatdb\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBpatmatdb\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Protein:Motifs" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqall\fR
+.RS 4
+.RE
+.SS "Required section"
+.PP
+\fB\-motif\fR \fIstring\fR
+.RS 4
+Patterns for patmatdb are based on the format of pattern used in the PROSITE database\&. For example: \*(Aq[DE](2)HS{P}X(2)PX(2,4)C\*(Aq means two Asps or Glus in any order followed by His, Ser, any residue other then Pro, then two of any residue followed by Pro followed by two to four of any residue followed by Cys\&. The search is case\-independent, so \*(AqAAA\*(Aq matches \*(Aqaaa\*(Aq\&.
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIreport\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+patmatdb is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/restrict.1e
+++ emboss-6.4.0/debian/manpages/restrict.1e
@@ -0,0 +1,161 @@
+'\" t
+.\"     Title: RESTRICT
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "RESTRICT" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+restrict \- Report restriction enzyme cleavage sites in a nucleotide sequence
+.SH "SYNOPSIS"
+.HP \w'\fBrestrict\fR\ 'u
+\fBrestrict\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-datafile\ \fR\fB\fIdatafile\fR\fR \fB\-mfile\ \fR\fB\fIdatafile\fR\fR \fB\-sitelen\ \fR\fB\fIinteger\fR\fR \fB\-enzymes\ \fR\fB\fIstring\fR\fR \fB\-min\ \fR\fB\fIinteger\fR\fR \fB\-max\ \fR\fB\fIinteger\fR\fR \fB\-solofragment\ \fR\fB\fIboolean\fR\fR \fB\-single\ \fR\fB\fIboolean\fR\fR \fB\-blunt\ \fR\fB\fIboolean\fR\fR \fB\-sticky\ \fR\fB\fIboolean\fR\fR \fB\-ambiguity\ \fR\fB\fIboolean\fR\fR \fB\-plasmid\ \fR\fB\fIboolean\fR\fR \fB\-methylation\ \fR\fB\fIboolean\fR\fR \fB\-commercial\ \fR\fB\fIboolean\fR\fR \fB\-limit\ \fR\fB\fIboolean\fR\fR \fB\-alphabetic\ \fR\fB\fIboolean\fR\fR \fB\-fragments\ \fR\fB\fIboolean\fR\fR \fB\-name\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIreport\fR\fR
+.HP \w'\fBrestrict\fR\ 'u
+\fBrestrict\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBrestrict\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Restriction" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqall\fR
+.RS 4
+.RE
+.PP
+\fB\-datafile\fR \fIdatafile\fR
+.RS 4
+.RE
+.PP
+\fB\-mfile\fR \fIdatafile\fR
+.RS 4
+Default value: Emethylsites\&.dat
+.RE
+.SS "Required section"
+.PP
+\fB\-sitelen\fR \fIinteger\fR
+.RS 4
+This sets the minimum length of the restriction enzyme recognition site\&. Any enzymes with sites shorter than this will be ignored\&. Default value: 4
+.RE
+.PP
+\fB\-enzymes\fR \fIstring\fR
+.RS 4
+The name \*(Aqall\*(Aq reads in all enzyme names from the REBASE database\&. You can specify enzymes by giving their names with commas between then, such as: \*(AqHincII,hinfI,ppiI,hindiii\*(Aq\&. The case of the names is not important\&. You can specify a file of enzyme names to read in by giving the name of the file holding the enzyme names with a \*(Aq@\*(Aq character in front of it, for example, \*(Aq@enz\&.list\*(Aq\&. Blank lines and lines starting with a hash character or \*(Aq!\*(Aq are ignored and all other lines are concatenated together with a comma character \*(Aq,\*(Aq and then treated as the list of enzymes to search for\&. An example of a file of enzyme names is: ! my enzymes HincII, ppiII ! other enzymes hindiii HinfI PpiI Default value: all
+.RE
+.SS "Advanced section"
+.PP
+\fB\-min\fR \fIinteger\fR
+.RS 4
+This sets the minimum number of cuts for any restriction enzyme that will be considered\&. Any enzymes that cut fewer times than this will be ignored\&. Default value: 1
+.RE
+.PP
+\fB\-max\fR \fIinteger\fR
+.RS 4
+This sets the maximum number of cuts for any restriction enzyme that will be considered\&. Any enzymes that cut more times than this will be ignored\&. Default value: 2000000000
+.RE
+.PP
+\fB\-solofragment\fR \fIboolean\fR
+.RS 4
+This gives the fragment lengths of the forward sense strand produced by complete restriction by each restriction enzyme on its own\&. Results are added to the tail section of the report\&. Default value: N
+.RE
+.PP
+\fB\-single\fR \fIboolean\fR
+.RS 4
+If this is set then this forces the values of the mincuts and maxcuts qualifiers to both be 1\&. Any other value you may have set them to will be ignored\&. Default value: N
+.RE
+.PP
+\fB\-blunt\fR \fIboolean\fR
+.RS 4
+This allows those enzymes which cut at the same position on the forward and reverse strands to be considered\&. Default value: Y
+.RE
+.PP
+\fB\-sticky\fR \fIboolean\fR
+.RS 4
+This allows those enzymes which cut at different positions on the forward and reverse strands, leaving an overhang, to be considered\&. Default value: Y
+.RE
+.PP
+\fB\-ambiguity\fR \fIboolean\fR
+.RS 4
+This allows those enzymes which have one or more \*(AqN\*(Aq ambiguity codes in their pattern to be considered Default value: Y
+.RE
+.PP
+\fB\-plasmid\fR \fIboolean\fR
+.RS 4
+If this is set then this allows searches for restriction enzyme recognition site and cut positions that span the end of the sequence to be considered\&. Default value: N
+.RE
+.PP
+\fB\-methylation\fR \fIboolean\fR
+.RS 4
+If this is set then RE recognition sites will not match methylated bases\&. Default value: N
+.RE
+.PP
+\fB\-commercial\fR \fIboolean\fR
+.RS 4
+If this is set, then only those enzymes with a commercial supplier will be searched for\&. This qualifier is ignored if you have specified an explicit list of enzymes to search for, rather than searching through \*(Aqall\*(Aq the enzymes in the REBASE database\&. It is assumed that, if you are asking for an explicit enzyme, then you probably know where to get it from and so all enzymes names that you have asked to be searched for, and which cut, will be reported whether or not they have a commercial supplier\&. Default value: Y
+.RE
+.SS "Output section"
+.PP
+\fB\-limit\fR \fIboolean\fR
+.RS 4
+This limits the reporting of enzymes to just one enzyme from each group of isoschizomers\&. The enzyme chosen to represent an isoschizomer group is the prototype indicated in the data file \*(Aqembossre\&.equ\*(Aq, which is created by the program \*(Aqrebaseextract\*(Aq\&. If you prefer different prototypes to be used, make a copy of embossre\&.equ in your home directory and edit it\&. If this value is set to be false then all of the input enzymes will be reported\&. You might like to set this to false if you are supplying an explicit set of enzymes rather than searching \*(Aqall\*(Aq of them\&. Default value: Y
+.RE
+.PP
+\fB\-alphabetic\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-fragments\fR \fIboolean\fR
+.RS 4
+This gives the fragment lengths of the forward sense strand produced by complete restriction using all of the input enzymes together\&. Results are added to the tail section of the report\&. Default value: N
+.RE
+.PP
+\fB\-name\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-outfile\fR \fIreport\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+restrict is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/dbiblast.1e
+++ emboss-6.4.0/debian/manpages/dbiblast.1e
@@ -0,0 +1,139 @@
+'\" t
+.\"     Title: DBIBLAST
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "DBIBLAST" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+dbiblast \- Index a BLAST database
+.SH "SYNOPSIS"
+.HP \w'\fBdbiblast\fR\ 'u
+\fBdbiblast\fR \fB\-dbname\ \fR\fB\fIstring\fR\fR \fB\-directory\ \fR\fB\fIdirectory\fR\fR \fB\-filenames\ \fR\fB\fIstring\fR\fR \fB\-release\ \fR\fB\fIstring\fR\fR \fB\-date\ \fR\fB\fIstring\fR\fR \fB\-seqtype\ \fR\fB\fIlist\fR\fR \fB\-blastversion\ \fR\fB\fIlist\fR\fR \fB\-fields\ \fR\fB\fIlist\fR\fR \fB\-exclude\ \fR\fB\fIstring\fR\fR \fB\-sortoptions\ \fR\fB\fIstring\fR\fR \fB\-maxindex\ \fR\fB\fIinteger\fR\fR \fB\-systemsort\ \fR\fB\fIboolean\fR\fR \fB\-cleanup\ \fR\fB\fIboolean\fR\fR \fB\-sourcefile\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR \fB\-indexoutdir\ \fR\fB\fIoutdir\fR\fR
+.HP \w'\fBdbiblast\fR\ 'u
+\fBdbiblast\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBdbiblast\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Database indexing" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-dbname\fR \fIstring\fR
+.RS 4
+.RE
+.PP
+\fB\-directory\fR \fIdirectory\fR
+.RS 4
+Default value: \&.
+.RE
+.PP
+\fB\-filenames\fR \fIstring\fR
+.RS 4
+Default value: $(dbname)
+.RE
+.SS "Required section"
+.PP
+\fB\-release\fR \fIstring\fR
+.RS 4
+Default value: 0\&.0
+.RE
+.PP
+\fB\-date\fR \fIstring\fR
+.RS 4
+Default value: 00/00/00
+.RE
+.PP
+\fB\-seqtype\fR \fIlist\fR
+.RS 4
+Default value: unknown
+.RE
+.PP
+\fB\-blastversion\fR \fIlist\fR
+.RS 4
+Default value: unknown
+.RE
+.SS "Advanced section"
+.PP
+\fB\-fields\fR \fIlist\fR
+.RS 4
+Default value: acc
+.RE
+.PP
+\fB\-exclude\fR \fIstring\fR
+.RS 4
+.RE
+.PP
+\fB\-sortoptions\fR \fIstring\fR
+.RS 4
+Sort options, typically \*(Aq\-T \&.\*(Aq to use current directory for work files and \*(Aq\-k 1,1\*(Aq to force GNU sort to use the first field Default value: \-T \&. \-k 1,1
+.RE
+.PP
+\fB\-maxindex\fR \fIinteger\fR
+.RS 4
+.RE
+.PP
+\fB\-systemsort\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-cleanup\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-sourcefile\fR \fIboolean\fR
+.RS 4
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.PP
+\fB\-indexoutdir\fR \fIoutdir\fR
+.RS 4
+Default value: \&.
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+dbiblast is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/tfscan.1e
+++ emboss-6.4.0/debian/manpages/tfscan.1e
@@ -0,0 +1,90 @@
+'\" t
+.\"     Title: TFSCAN
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "TFSCAN" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+tfscan \- Identify transcription factor binding sites in DNA sequences
+.SH "SYNOPSIS"
+.HP \w'\fBtfscan\fR\ 'u
+\fBtfscan\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-menu\ \fR\fB\fIlist\fR\fR \fB\-custom\ \fR\fB\fIdatafile\fR\fR \fB\-mismatch\ \fR\fB\fIinteger\fR\fR [\fB\-minlength\ \fR\fB\fIinteger\fR\fR] \fB\-outfile\ \fR\fB\fIreport\fR\fR
+.HP \w'\fBtfscan\fR\ 'u
+\fBtfscan\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBtfscan\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Transcription" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqall\fR
+.RS 4
+.RE
+.PP
+\fB\-menu\fR \fIlist\fR
+.RS 4
+Default value: V
+.RE
+.PP
+\fB\-custom\fR \fIdatafile\fR
+.RS 4
+.RE
+.SS "Required section"
+.PP
+\fB\-mismatch\fR \fIinteger\fR
+.RS 4
+.RE
+.SS "Additional section"
+.PP
+\fB\-minlength\fR \fIinteger\fR
+.RS 4
+Default value: 1
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIreport\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+tfscan is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/texttotext.1e
+++ emboss-6.4.0/debian/manpages/texttotext.1e
@@ -0,0 +1,93 @@
+'\" t
+.\"     Title: TEXTTOTEXT
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "TEXTTOTEXT" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+texttotext \- Convert a plain text format to a different format
+.SH "SYNOPSIS"
+.HP \w'\fBtexttotext\fR\ 'u
+\fBtexttotext\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR \fB\-type\ \fR\fB\fIlist\fR\fR \fB\-seq\ \fR\fB\fIlist\fR\fR \fB\-feat\ \fR\fB\fIlist\fR\fR \fB\-align\ \fR\fB\fIlist\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBtexttotext\fR\ 'u
+\fBtexttotext\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBtexttotext\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Misc" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-infile\fR \fIinfile\fR
+.RS 4
+.RE
+.SS "Required section"
+.PP
+\fB\-type\fR \fIlist\fR
+.RS 4
+You must specify the type of file content so that appropriate output format options may be generated\&.
+.RE
+.PP
+\fB\-seq\fR \fIlist\fR
+.RS 4
+This option sets the format of a sequence output file\&. Default value: X
+.RE
+.PP
+\fB\-feat\fR \fIlist\fR
+.RS 4
+This option sets the format of a sequence feature output file\&. Default value: X
+.RE
+.PP
+\fB\-align\fR \fIlist\fR
+.RS 4
+This option sets the format of a sequence alignment output file\&. Default value: X
+.RE
+.SS "Additional section"
+.SS "Advanced section"
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+texttotext is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/findkm.1e
+++ emboss-6.4.0/debian/manpages/findkm.1e
@@ -0,0 +1,80 @@
+'\" t
+.\"     Title: FINDKM
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "FINDKM" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+findkm \- Calculate and plot enzyme reaction data
+.SH "SYNOPSIS"
+.HP \w'\fBfindkm\fR\ 'u
+\fBfindkm\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR \fB\-plot\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR \fB\-graphlb\ \fR\fB\fIxygraph\fR\fR
+.HP \w'\fBfindkm\fR\ 'u
+\fBfindkm\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBfindkm\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Enzyme Kinetics" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-infile\fR \fIinfile\fR
+.RS 4
+.RE
+.SS "Advanced section"
+.PP
+\fB\-plot\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.PP
+\fB\-graphlb\fR \fIxygraph\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+findkm is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/getorf.1e
+++ emboss-6.4.0/debian/manpages/getorf.1e
@@ -0,0 +1,111 @@
+'\" t
+.\"     Title: GETORF
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "GETORF" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+getorf \- Finds and extracts open reading frames (ORFs)
+.SH "SYNOPSIS"
+.HP \w'\fBgetorf\fR\ 'u
+\fBgetorf\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR [\fB\-table\ \fR\fB\fIlist\fR\fR] [\fB\-minsize\ \fR\fB\fIinteger\fR\fR] [\fB\-maxsize\ \fR\fB\fIinteger\fR\fR] [\fB\-find\ \fR\fB\fIlist\fR\fR] \fB\-methionine\ \fR\fB\fIboolean\fR\fR \fB\-circular\ \fR\fB\fIboolean\fR\fR \fB\-reverse\ \fR\fB\fIboolean\fR\fR \fB\-flanking\ \fR\fB\fIinteger\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR
+.HP \w'\fBgetorf\fR\ 'u
+\fBgetorf\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBgetorf\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Gene finding" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqall\fR
+.RS 4
+.RE
+.SS "Additional section"
+.PP
+\fB\-table\fR \fIlist\fR
+.RS 4
+.RE
+.PP
+\fB\-minsize\fR \fIinteger\fR
+.RS 4
+Default value: 30
+.RE
+.PP
+\fB\-maxsize\fR \fIinteger\fR
+.RS 4
+Default value: 1000000
+.RE
+.PP
+\fB\-find\fR \fIlist\fR
+.RS 4
+This is a small menu of possible output options\&. The first four options are to select either the protein translation or the original nucleic acid sequence of the open reading frame\&. There are two possible definitions of an open reading frame: it can either be a region that is free of STOP codons or a region that begins with a START codon and ends with a STOP codon\&. The last three options are probably only of interest to people who wish to investigate the statistical properties of the regions around potential START or STOP codons\&. The last option assumes that ORF lengths are calculated between two STOP codons\&.
+.RE
+.SS "Advanced section"
+.PP
+\fB\-methionine\fR \fIboolean\fR
+.RS 4
+START codons at the beginning of protein products will usually code for Methionine, despite what the codon will code for when it is internal to a protein\&. This qualifier sets all such START codons to code for Methionine by default\&. Default value: Y
+.RE
+.PP
+\fB\-circular\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-reverse\fR \fIboolean\fR
+.RS 4
+Set this to be false if you do not wish to find ORFs in the reverse complement of the sequence\&. Default value: Y
+.RE
+.PP
+\fB\-flanking\fR \fIinteger\fR
+.RS 4
+If you have chosen one of the options of the type of sequence to find that gives the flanking sequence around a STOP or START codon, this allows you to set the number of nucleotides either side of that codon to output\&. If the region of flanking nucleotides crosses the start or end of the sequence, no output is given for this codon\&. Default value: 100
+.RE
+.SS "Output section"
+.PP
+\fB\-outseq\fR \fIseqoutall\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+getorf is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/pepinfo.1e
+++ emboss-6.4.0/debian/manpages/pepinfo.1e
@@ -0,0 +1,100 @@
+'\" t
+.\"     Title: PEPINFO
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "PEPINFO" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+pepinfo \- Plot amino acid properties of a protein sequence in parallel\&.
+.SH "SYNOPSIS"
+.HP \w'\fBpepinfo\fR\ 'u
+\fBpepinfo\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR [\fB\-aaproperties\ \fR\fB\fIdatafile\fR\fR] [\fB\-aahydropathy\ \fR\fB\fIdatafile\fR\fR] [\fB\-hwindow\ \fR\fB\fIinteger\fR\fR] \fB\-graph\ \fR\fB\fIxygraph\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR \fB\-generalplot\ \fR\fB\fIboolean\fR\fR \fB\-hydropathyplot\ \fR\fB\fIboolean\fR\fR
+.HP \w'\fBpepinfo\fR\ 'u
+\fBpepinfo\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBpepinfo\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Protein:Composition,Protein:Properties,Display" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIsequence\fR
+.RS 4
+.RE
+.PP
+\fB\-aaproperties\fR \fIdatafile\fR
+.RS 4
+Default value: Eaa_properties\&.dat
+.RE
+.PP
+\fB\-aahydropathy\fR \fIdatafile\fR
+.RS 4
+Default value: Eaa_hydropathy\&.dat
+.RE
+.SS "Additional section"
+.PP
+\fB\-hwindow\fR \fIinteger\fR
+.RS 4
+Default value: 9
+.RE
+.SS "Output section"
+.PP
+\fB\-graph\fR \fIxygraph\fR
+.RS 4
+.RE
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.PP
+\fB\-generalplot\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-hydropathyplot\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+pepinfo is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/seqret.1e
+++ emboss-6.4.0/debian/manpages/seqret.1e
@@ -0,0 +1,80 @@
+'\" t
+.\"     Title: SEQRET
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "SEQRET" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+seqret \- Reads and writes (returns) sequences
+.SH "SYNOPSIS"
+.HP \w'\fBseqret\fR\ 'u
+\fBseqret\fR \fB\-feature\ \fR\fB\fIboolean\fR\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-firstonly\ \fR\fB\fIboolean\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR
+.HP \w'\fBseqret\fR\ 'u
+\fBseqret\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBseqret\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Data retrieval,Edit" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-feature\fR \fIboolean\fR
+.RS 4
+.RE
+.PP
+\fB\-sequence\fR \fIseqall\fR
+.RS 4
+.RE
+.SS "Advanced section"
+.PP
+\fB\-firstonly\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.SS "Output section"
+.PP
+\fB\-outseq\fR \fIseqoutall\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+seqret is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/backtranambig.1e
+++ emboss-6.4.0/debian/manpages/backtranambig.1e
@@ -0,0 +1,75 @@
+'\" t
+.\"     Title: BACKTRANAMBIG
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "BACKTRANAMBIG" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+backtranambig \- Back\-translate a protein sequence to ambiguous nucleotide sequence
+.SH "SYNOPSIS"
+.HP \w'\fBbacktranambig\fR\ 'u
+\fBbacktranambig\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR [\fB\-table\ \fR\fB\fIlist\fR\fR] \fB\-outfile\ \fR\fB\fIseqoutall\fR\fR
+.HP \w'\fBbacktranambig\fR\ 'u
+\fBbacktranambig\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBbacktranambig\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Translation,Protein:Composition" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqall\fR
+.RS 4
+.RE
+.SS "Additional section"
+.PP
+\fB\-table\fR \fIlist\fR
+.RS 4
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIseqoutall\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+backtranambig is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/domtestc.1e
+++ emboss-6.4.0/debian/manpages/domtestc.1e
@@ -0,0 +1,65 @@
+'\" t
+.\"     Title: DOMTESTC
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "DOMTESTC" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+domtestc \- Create and write out some typical XML
+.SH "SYNOPSIS"
+.HP \w'\fBdomtestc\fR\ 'u
+\fBdomtestc\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBdomtestc\fR\ 'u
+\fBdomtestc\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBdomtestc\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&.
+.SH "OPTIONS"
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+domtestc is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/dbxreport.1e
+++ emboss-6.4.0/debian/manpages/dbxreport.1e
@@ -0,0 +1,86 @@
+'\" t
+.\"     Title: DBXREPORT
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "DBXREPORT" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+dbxreport \- Validate index and report internals for dbx databases
+.SH "SYNOPSIS"
+.HP \w'\fBdbxreport\fR\ 'u
+\fBdbxreport\fR \fB\-dbname\ \fR\fB\fIstring\fR\fR \fB\-fields\ \fR\fB\fIstring\fR\fR \fB\-indexdir\ \fR\fB\fIdirectory\fR\fR \fB\-fullreport\ \fR\fB\fIboolean\fR\fR \fB\-$(dbname)\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBdbxreport\fR\ 'u
+\fBdbxreport\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBdbxreport\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Database indexing" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-dbname\fR \fIstring\fR
+.RS 4
+.RE
+.PP
+\fB\-fields\fR \fIstring\fR
+.RS 4
+A list of index fields separated by spaces or commas\&. Default value: id
+.RE
+.PP
+\fB\-indexdir\fR \fIdirectory\fR
+.RS 4
+.RE
+.SS "Required section"
+.SS "Advanced section"
+.PP
+\fB\-fullreport\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.SS "Output section"
+.PP
+\fB\-$(dbname)\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+dbxreport is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/edamisformat.1e
+++ emboss-6.4.0/debian/manpages/edamisformat.1e
@@ -0,0 +1,92 @@
+'\" t
+.\"     Title: EDAMISFORMAT
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "EDAMISFORMAT" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+edamisformat \- Find EDAM ontology terms by is_format_of relation
+.SH "SYNOPSIS"
+.HP \w'\fBedamisformat\fR\ 'u
+\fBedamisformat\fR \fB\-identifier\ \fR\fB\fIstring\fR\fR [\fB\-namespace\ \fR\fB\fIlist\fR\fR] \fB\-sensitive\ \fR\fB\fIboolean\fR\fR \fB\-subclasses\ \fR\fB\fIboolean\fR\fR \fB\-obsolete\ \fR\fB\fIboolean\fR\fR \fB\-edamisformat\ \fR\fB\fIoutobo\fR\fR
+.HP \w'\fBedamisformat\fR\ 'u
+\fBedamisformat\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBedamisformat\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Ontology:EDAM,Data retrieval:Ontology data" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-identifier\fR \fIstring\fR
+.RS 4
+.RE
+.SS "Additional section"
+.PP
+\fB\-namespace\fR \fIlist\fR
+.RS 4
+By default all terms are returned\&. Searches can be limited to one or a few namespaces\&. Default value: *
+.RE
+.SS "Advanced section"
+.PP
+\fB\-sensitive\fR \fIboolean\fR
+.RS 4
+By default, the query keywords are matched against the EDAM term names (and synonyms) only\&. This option also matches the keywords against the EDAM term definitions and will therefore (typically) report more matches\&. Default value: N
+.RE
+.PP
+\fB\-subclasses\fR \fIboolean\fR
+.RS 4
+Extend the query matches to include all terms which are specialisations (EDAM sub\-classes) of the matched type\&. Default value: N
+.RE
+.PP
+\fB\-obsolete\fR \fIboolean\fR
+.RS 4
+The default behaviour is to not use or return obsolete terms\&. This option if set will include all terms\&. Default value: N
+.RE
+.SS "Output section"
+.PP
+\fB\-edamisformat\fR \fIoutobo\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+edamisformat is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/entrails.1e
+++ emboss-6.4.0/debian/manpages/entrails.1e
@@ -0,0 +1,71 @@
+'\" t
+.\"     Title: ENTRAILS
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "ENTRAILS" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+entrails \- Reports the internal data from the EMBOSS code
+.SH "SYNOPSIS"
+.HP \w'\fBentrails\fR\ 'u
+\fBentrails\fR [\fB\-fullreport\ \fR\fB\fIboolean\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBentrails\fR\ 'u
+\fBentrails\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBentrails\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Misc" command group(s)\&.
+.SH "OPTIONS"
+.SS "Additional section"
+.PP
+\fB\-fullreport\fR \fIboolean\fR
+.RS 4
+By default, only the essential details are reported Default value: N
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+entrails is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/entret.1e
+++ emboss-6.4.0/debian/manpages/entret.1e
@@ -0,0 +1,75 @@
+'\" t
+.\"     Title: ENTRET
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "ENTRET" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+entret \- Retrieves sequence entries from flatfile databases and files
+.SH "SYNOPSIS"
+.HP \w'\fBentret\fR\ 'u
+\fBentret\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-firstonly\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBentret\fR\ 'u
+\fBentret\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBentret\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit,Data retrieval:Sequence data,Data retrieval:Text data" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqall\fR
+.RS 4
+.RE
+.SS "Advanced section"
+.PP
+\fB\-firstonly\fR \fIboolean\fR
+.RS 4
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+entret is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/acdtable.1e
+++ emboss-6.4.0/debian/manpages/acdtable.1e
@@ -0,0 +1,60 @@
+'\" t
+.\"     Title: ACDTABLE
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "ACDTABLE" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+acdtable \- Generate an HTML table of parameters from an application ACD file
+.SH "SYNOPSIS"
+.HP \w'\fBacdtable\fR\ 'u
+\fBacdtable\fR
+.HP \w'\fBacdtable\fR\ 'u
+\fBacdtable\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBacdtable\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Acd,Data retrieval:Tool data" command group(s)\&.
+.SH "OPTIONS"
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+acdtable is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/plotorf.1e
+++ emboss-6.4.0/debian/manpages/plotorf.1e
@@ -0,0 +1,81 @@
+'\" t
+.\"     Title: PLOTORF
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "PLOTORF" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+plotorf \- Plot potential open reading frames in a nucleotide sequence
+.SH "SYNOPSIS"
+.HP \w'\fBplotorf\fR\ 'u
+\fBplotorf\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR \fB\-start\ \fR\fB\fIstring\fR\fR \fB\-stop\ \fR\fB\fIstring\fR\fR \fB\-graph\ \fR\fB\fIxygraph\fR\fR
+.HP \w'\fBplotorf\fR\ 'u
+\fBplotorf\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBplotorf\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Gene finding,Nucleic:Translation,Display" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIsequence\fR
+.RS 4
+.RE
+.SS "Advanced section"
+.PP
+\fB\-start\fR \fIstring\fR
+.RS 4
+Default value: ATG
+.RE
+.PP
+\fB\-stop\fR \fIstring\fR
+.RS 4
+Default value: TAA,TAG,TGA
+.RE
+.SS "Output section"
+.PP
+\fB\-graph\fR \fIxygraph\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+plotorf is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/testplot.1e
+++ emboss-6.4.0/debian/manpages/testplot.1e
@@ -0,0 +1,76 @@
+'\" t
+.\"     Title: TESTPLOT
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "TESTPLOT" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+testplot \- Test plot
+.SH "SYNOPSIS"
+.HP \w'\fBtestplot\fR\ 'u
+\fBtestplot\fR \fB\-points\ \fR\fB\fIinteger\fR\fR \fB\-overlap\ \fR\fB\fIboolean\fR\fR \fB\-graph\ \fR\fB\fIxygraph\fR\fR
+.HP \w'\fBtestplot\fR\ 'u
+\fBtestplot\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBtestplot\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Test" command group(s)\&.
+.SH "OPTIONS"
+.SS "Required section"
+.PP
+\fB\-points\fR \fIinteger\fR
+.RS 4
+Default value: 90
+.RE
+.SS "Output section"
+.PP
+\fB\-overlap\fR \fIboolean\fR
+.RS 4
+Default value: y
+.RE
+.PP
+\fB\-graph\fR \fIxygraph\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+testplot is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/sirna.1e
+++ emboss-6.4.0/debian/manpages/sirna.1e
@@ -0,0 +1,102 @@
+'\" t
+.\"     Title: SIRNA
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "SIRNA" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+sirna \- Finds siRNA duplexes in mRNA
+.SH "SYNOPSIS"
+.HP \w'\fBsirna\fR\ 'u
+\fBsirna\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR [\fB\-poliii\ \fR\fB\fIboolean\fR\fR] [\fB\-aa\ \fR\fB\fIboolean\fR\fR] [\fB\-tt\ \fR\fB\fIboolean\fR\fR] [\fB\-polybase\ \fR\fB\fIboolean\fR\fR] \fB\-outfile\ \fR\fB\fIreport\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR [\fB\-context\ \fR\fB\fIboolean\fR\fR]
+.HP \w'\fBsirna\fR\ 'u
+\fBsirna\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBsirna\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Functional sites,Nucleic:2D structure" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqall\fR
+.RS 4
+.RE
+.SS "Sequence input options"
+.PP
+\fB\-poliii\fR \fIboolean\fR
+.RS 4
+This option allows you to select only the 21 base probes that start with a purine and so can be expressed from Pol III expression vectors\&. This is the NARN(17)YNN pattern that has been suggested by Tuschl et al\&. Default value: N
+.RE
+.PP
+\fB\-aa\fR \fIboolean\fR
+.RS 4
+This option allows you to select only those 23 base regions that start with AA\&. If this option is not selected then regions that start with AA will be favoured by giving them a higher score, but regions that do not start with AA will also be reported\&. Default value: N
+.RE
+.PP
+\fB\-tt\fR \fIboolean\fR
+.RS 4
+This option allows you to select only those 23 base regions that end with TT\&. If this option is not selected then regions that end with TT will be favoured by giving them a higher score, but regions that do not end with TT will also be reported\&. Default value: N
+.RE
+.PP
+\fB\-polybase\fR \fIboolean\fR
+.RS 4
+If this option is FALSE then only those 23 base regions that have no repeat of 4 or more of any bases in a row will be reported\&. No regions will ever be reported that have 4 or more G\*(Aqs in a row\&. Default value: Y
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIreport\fR
+.RS 4
+The output is a table of the forward and reverse parts of the 21 base siRNA duplex\&. Both the forward and reverse sequences are written 5\*(Aq to 3\*(Aq, ready to be ordered\&. The last two bases have been replaced by \*(AqdTdT\*(Aq\&. The starting position of the 23 base region and the %GC content is also given\&. If you wish to see the complete 23 base sequence, then either look at the sequence in the other output file, or use the qualifier \*(Aq\-context\*(Aq which will display the 23 bases of the forward sequence in this report with the first two bases in brackets\&. These first two bases do not form part of the siRNA probe to be ordered\&.
+.RE
+.PP
+\fB\-outseq\fR \fIseqoutall\fR
+.RS 4
+This is a file of the sequences of the 23 base regions that the siRNAs are selected from\&. You may use it to do searches of mRNA databases (e\&.g\&. REFSEQ) to confirm that the probes are unique to the gene you wish to use it on\&.
+.RE
+.PP
+\fB\-context\fR \fIboolean\fR
+.RS 4
+The output report file gives the sequences of the 21 base siRNA regions ready to be ordered\&. This does not give you an indication of the 2 bases before the 21 bases\&. It is often interesting to see which of the suggested possible probe regions have an \*(AqAA\*(Aq in front of them (i\&.e\&. it is useful to see which of the 23 base regions start with an \*(AqAA\*(Aq)\&. This option displays the whole 23 bases of the region with the first two bases in brackets, e\&.g\&. \*(Aq(AA)\*(Aq to give you some context for the probe region\&. YOU SHOULD NOT INCLUDE THE TWO BASES IN BRACKETS WHEN YOU PLACE AN ORDER FOR THE PROBES\&. Default value: N
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+sirna is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/splitsource.1e
+++ emboss-6.4.0/debian/manpages/splitsource.1e
@@ -0,0 +1,77 @@
+'\" t
+.\"     Title: SPLITSOURCE
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "SPLITSOURCE" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+splitsource \- Split sequence(s) into original source sequences
+.SH "SYNOPSIS"
+.HP \w'\fBsplitsource\fR\ 'u
+\fBsplitsource\fR \fB\-feature\ \fR\fB\fIboolean\fR\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR
+.HP \w'\fBsplitsource\fR\ 'u
+\fBsplitsource\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBsplitsource\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-feature\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-sequence\fR \fIseqall\fR
+.RS 4
+.RE
+.SS "Additional section"
+.SS "Advanced section"
+.SS "Output section"
+.PP
+\fB\-outseq\fR \fIseqoutall\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+splitsource is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/textget.1e
+++ emboss-6.4.0/debian/manpages/textget.1e
@@ -0,0 +1,72 @@
+'\" t
+.\"     Title: TEXTGET
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "TEXTGET" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+textget \- Get text data entries
+.SH "SYNOPSIS"
+.HP \w'\fBtextget\fR\ 'u
+\fBtextget\fR \fB\-text\ \fR\fB\fItext\fR\fR \fB\-outfile\ \fR\fB\fIouttext\fR\fR
+.HP \w'\fBtextget\fR\ 'u
+\fBtextget\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBtextget\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Data retrieval:Text data" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-text\fR \fItext\fR
+.RS 4
+.RE
+.SS "Additional section"
+.SS "Advanced section"
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIouttext\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+textget is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/notseq.1e
+++ emboss-6.4.0/debian/manpages/notseq.1e
@@ -0,0 +1,81 @@
+'\" t
+.\"     Title: NOTSEQ
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "NOTSEQ" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+notseq \- Write to file a subset of an input stream of sequences
+.SH "SYNOPSIS"
+.HP \w'\fBnotseq\fR\ 'u
+\fBnotseq\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-exclude\ \fR\fB\fIstring\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR [\fB\-junkoutseq\ \fR\fB\fIseqoutall\fR\fR]
+.HP \w'\fBnotseq\fR\ 'u
+\fBnotseq\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBnotseq\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqall\fR
+.RS 4
+.RE
+.SS "Required section"
+.PP
+\fB\-exclude\fR \fIstring\fR
+.RS 4
+Enter a list of sequence names or accession numbers to exclude from the sequences read in\&. The excluded sequences will be written to the file specified in the \*(Aqjunkout\*(Aq parameter\&. The remainder will be written out to the file specified in the \*(Aqoutseq\*(Aq parameter\&. The list of sequence names can be separated by either spaces or commas\&. The sequence names can be wildcarded\&. The sequence names are case independent\&. An example of a list of sequences to be excluded is: myseq, hs*, one two three a file containing a list of sequence names can be specified by giving the file name preceeded by a \*(Aq@\*(Aq, eg: \*(Aq@names\&.dat\*(Aq
+.RE
+.SS "Output section"
+.PP
+\fB\-outseq\fR \fIseqoutall\fR
+.RS 4
+.RE
+.PP
+\fB\-junkoutseq\fR \fIseqoutall\fR
+.RS 4
+This file collects the sequences which you have excluded from the main output file of sequences\&. Default value: /dev/null
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+notseq is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/complex.1e
+++ emboss-6.4.0/debian/manpages/complex.1e
@@ -0,0 +1,120 @@
+'\" t
+.\"     Title: COMPLEX
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "COMPLEX" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+complex \- Find the linguistic complexity in nucleotide sequences
+.SH "SYNOPSIS"
+.HP \w'\fBcomplex\fR\ 'u
+\fBcomplex\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-lwin\ \fR\fB\fIinteger\fR\fR \fB\-step\ \fR\fB\fIinteger\fR\fR \fB\-jmin\ \fR\fB\fIinteger\fR\fR \fB\-jmax\ \fR\fB\fIinteger\fR\fR \fB\-omnia\ \fR\fB\fItoggle\fR\fR \fB\-sim\ \fR\fB\fIinteger\fR\fR \fB\-freq\ \fR\fB\fIboolean\fR\fR \fB\-print\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR \fB\-ujtablefile\ \fR\fB\fIoutfile\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR
+.HP \w'\fBcomplex\fR\ 'u
+\fBcomplex\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBcomplex\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Composition" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqall\fR
+.RS 4
+.RE
+.PP
+\fB\-lwin\fR \fIinteger\fR
+.RS 4
+Default value: 100
+.RE
+.PP
+\fB\-step\fR \fIinteger\fR
+.RS 4
+Displacement of the window over the sequence Default value: 5
+.RE
+.PP
+\fB\-jmin\fR \fIinteger\fR
+.RS 4
+Default value: 4
+.RE
+.PP
+\fB\-jmax\fR \fIinteger\fR
+.RS 4
+Default value: 6
+.RE
+.SS "Advanced section"
+.PP
+\fB\-omnia\fR \fItoggle\fR
+.RS 4
+Calculate over a set of sequences Default value: N
+.RE
+.PP
+\fB\-sim\fR \fIinteger\fR
+.RS 4
+Calculate the linguistic complexity by comparison with a number of simulations having a uniform distribution of bases
+.RE
+.PP
+\fB\-freq\fR \fIboolean\fR
+.RS 4
+Execute the simulation of a sequence based on the base frequency of the original sequence Default value: N
+.RE
+.SS "Output section"
+.PP
+\fB\-print\fR \fIboolean\fR
+.RS 4
+Generate a file named UjTable containing the values of Uj for each word j in the real sequence(s) and in any simulated sequences Default value: N
+.RE
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.PP
+\fB\-ujtablefile\fR \fIoutfile\fR
+.RS 4
+Default value: complex\&.ujtable
+.RE
+.PP
+\fB\-outseq\fR \fIseqoutall\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+complex is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/acdvalid.1e
+++ emboss-6.4.0/debian/manpages/acdvalid.1e
@@ -0,0 +1,60 @@
+'\" t
+.\"     Title: ACDVALID
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "ACDVALID" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+acdvalid \- Validate an application ACD file
+.SH "SYNOPSIS"
+.HP \w'\fBacdvalid\fR\ 'u
+\fBacdvalid\fR
+.HP \w'\fBacdvalid\fR\ 'u
+\fBacdvalid\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBacdvalid\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Acd,Data retrieval:Tool data" command group(s)\&.
+.SH "OPTIONS"
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+acdvalid is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/extractseq.1e
+++ emboss-6.4.0/debian/manpages/extractseq.1e
@@ -0,0 +1,82 @@
+'\" t
+.\"     Title: EXTRACTSEQ
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "EXTRACTSEQ" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+extractseq \- Extract regions from a sequence
+.SH "SYNOPSIS"
+.HP \w'\fBextractseq\fR\ 'u
+\fBextractseq\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR \fB\-regions\ \fR\fB\fIrange\fR\fR [\fB\-separate\ \fR\fB\fIboolean\fR\fR] \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR
+.HP \w'\fBextractseq\fR\ 'u
+\fBextractseq\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBextractseq\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIsequence\fR
+.RS 4
+.RE
+.SS "Required section"
+.PP
+\fB\-regions\fR \fIrange\fR
+.RS 4
+Regions to extract\&. A set of regions is specified by a set of pairs of positions\&. The positions are integers\&. They are separated by any non\-digit, non\-alpha character\&. Examples of region specifications are: 24\-45, 56\-78 1:45, 67=99;765\&.\&.888 1,5,8,10,23,45,57,99 Default value: $(sequence\&.begin)\-$(sequence\&.end)
+.RE
+.SS "Additional section"
+.PP
+\fB\-separate\fR \fIboolean\fR
+.RS 4
+If this is set true then each specified region is written out as a separate sequence\&. The name of the sequence is created from the name of the original sequence with the start and end positions of the range appended with underscore characters between them, eg: XYZ region 2 to 34 is written as: XYZ_2_34 Default value: N
+.RE
+.SS "Output section"
+.PP
+\fB\-outseq\fR \fIseqoutall\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+extractseq is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/trimspace.1e
+++ emboss-6.4.0/debian/manpages/trimspace.1e
@@ -0,0 +1,73 @@
+'\" t
+.\"     Title: TRIMSPACE
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "TRIMSPACE" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+trimspace \- Remove extra whitespace from an ASCII text file
+.SH "SYNOPSIS"
+.HP \w'\fBtrimspace\fR\ 'u
+\fBtrimspace\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBtrimspace\fR\ 'u
+\fBtrimspace\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBtrimspace\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-infile\fR \fIinfile\fR
+.RS 4
+.RE
+.SS "Required section"
+.SS "Additional section"
+.SS "Advanced section"
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+trimspace is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/tranalign.1e
+++ emboss-6.4.0/debian/manpages/tranalign.1e
@@ -0,0 +1,79 @@
+'\" t
+.\"     Title: TRANALIGN
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "TRANALIGN" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+tranalign \- Generate an alignment of nucleic coding regions from aligned proteins
+.SH "SYNOPSIS"
+.HP \w'\fBtranalign\fR\ 'u
+\fBtranalign\fR \fB\-asequence\ \fR\fB\fIseqall\fR\fR \fB\-bsequence\ \fR\fB\fIseqset\fR\fR [\fB\-table\ \fR\fB\fIlist\fR\fR] \fB\-outseq\ \fR\fB\fIseqoutset\fR\fR
+.HP \w'\fBtranalign\fR\ 'u
+\fBtranalign\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBtranalign\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Alignment:Multiple" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-asequence\fR \fIseqall\fR
+.RS 4
+.RE
+.PP
+\fB\-bsequence\fR \fIseqset\fR
+.RS 4
+.RE
+.SS "Additional section"
+.PP
+\fB\-table\fR \fIlist\fR
+.RS 4
+.RE
+.SS "Output section"
+.PP
+\fB\-outseq\fR \fIseqoutset\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+tranalign is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/ontogetcommon.1e
+++ emboss-6.4.0/debian/manpages/ontogetcommon.1e
@@ -0,0 +1,77 @@
+'\" t
+.\"     Title: ONTOGETCOMMON
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "ONTOGETCOMMON" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+ontogetcommon \- Get common ancestor for terms
+.SH "SYNOPSIS"
+.HP \w'\fBontogetcommon\fR\ 'u
+\fBontogetcommon\fR \fB\-oboterms\ \fR\fB\fIobo\fR\fR [\fB\-obsolete\ \fR\fB\fIboolean\fR\fR] \fB\-ontogetcommon\ \fR\fB\fIoutobo\fR\fR
+.HP \w'\fBontogetcommon\fR\ 'u
+\fBontogetcommon\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBontogetcommon\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Ontology,Data retrieval:Ontology data" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-oboterms\fR \fIobo\fR
+.RS 4
+.RE
+.SS "Additional section"
+.PP
+\fB\-obsolete\fR \fIboolean\fR
+.RS 4
+The default behaviour is to not use or return obsolete terms\&. This option if set will include all terms\&. Default value: N
+.RE
+.SS "Advanced section"
+.SS "Output section"
+.PP
+\fB\-ontogetcommon\fR \fIoutobo\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+ontogetcommon is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/seqretset.1e
+++ emboss-6.4.0/debian/manpages/seqretset.1e
@@ -0,0 +1,74 @@
+'\" t
+.\"     Title: SEQRETSET
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "SEQRETSET" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+seqretset \- Reads and writes (returns) a set of sequences all at once
+.SH "SYNOPSIS"
+.HP \w'\fBseqretset\fR\ 'u
+\fBseqretset\fR \fB\-feature\ \fR\fB\fIboolean\fR\fR \fB\-sequence\ \fR\fB\fIseqset\fR\fR \fB\-outseq\ \fR\fB\fIseqoutset\fR\fR
+.HP \w'\fBseqretset\fR\ 'u
+\fBseqretset\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBseqretset\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-feature\fR \fIboolean\fR
+.RS 4
+.RE
+.PP
+\fB\-sequence\fR \fIseqset\fR
+.RS 4
+.RE
+.SS "Output section"
+.PP
+\fB\-outseq\fR \fIseqoutset\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+seqretset is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/emma.1e
+++ emboss-6.4.0/debian/manpages/emma.1e
@@ -0,0 +1,214 @@
+'\" t
+.\"     Title: EMMA
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "EMMA" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+emma \- Multiple sequence alignment (ClustalW wrapper)
+.SH "SYNOPSIS"
+.HP \w'\fBemma\fR\ 'u
+\fBemma\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR [\fB\-onlydend\ \fR\fB\fItoggle\fR\fR] \fB\-dend\ \fR\fB\fItoggle\fR\fR \fB\-dendfile\ \fR\fB\fIinfile\fR\fR [\fB\-slow\ \fR\fB\fItoggle\fR\fR] \fB\-pwmatrix\ \fR\fB\fIlist\fR\fR \fB\-pwdnamatrix\ \fR\fB\fIlist\fR\fR \fB\-usermatrix\ \fR\fB\fIvariable\fR\fR \fB\-pairwisedatafile\ \fR\fB\fIinfile\fR\fR \fB\-matrix\ \fR\fB\fIlist\fR\fR \fB\-usermamatrix\ \fR\fB\fIvariable\fR\fR \fB\-dnamatrix\ \fR\fB\fIlist\fR\fR \fB\-umamatrix\ \fR\fB\fIvariable\fR\fR \fB\-mamatrixfile\ \fR\fB\fIinfile\fR\fR \fB\-pwgapopen\ \fR\fB\fIfloat\fR\fR \fB\-pwgapextend\ \fR\fB\fIfloat\fR\fR \fB\-ktup\ \fR\fB\fIinteger\fR\fR \fB\-gapw\ \fR\fB\fIinteger\fR\fR \fB\-topdiags\ \fR\fB\fIinteger\fR\fR \fB\-window\ \fR\fB\fIinteger\fR\fR \fB\-nopercent\ \fR\fB\fIboolean\fR\fR [\fB\-gapopen\ \fR\fB\fIfloat\fR\fR] [\fB\-gapextend\ \fR\fB\fIfloat\fR\fR] [\fB\-endgaps\ \fR\fB\fIboolean\fR\fR] [\fB\-gapdist\ \fR\fB\fIinteger\fR\fR] \fB\-norgap\ \fR\fB\fIboolean\fR\fR \fB\-hgapres\ \fR\fB\fIstring\fR\fR \fB\-nohgap\ \fR\fB\fIboolean\fR\fR [\fB\-maxdiv\ \fR\fB\fIinteger\fR\fR] \fB\-outseq\ \fR\fB\fIseqoutset\fR\fR \fB\-dendoutfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBemma\fR\ 'u
+\fBemma\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBemma\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Alignment:Multiple" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqall\fR
+.RS 4
+.RE
+.PP
+\fB\-onlydend\fR \fItoggle\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-dend\fR \fItoggle\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-dendfile\fR \fIinfile\fR
+.RS 4
+.RE
+.PP
+\fB\-slow\fR \fItoggle\fR
+.RS 4
+A distance is calculated between every pair of sequences and these are used to construct the dendrogram which guides the final multiple alignment\&. The scores are calculated from separate pairwise alignments\&. These can be calculated using 2 methods: dynamic programming (slow but accurate) or by the method of Wilbur and Lipman (extremely fast but approximate)\&. The slow\-accurate method is fine for short sequences but will be VERY SLOW for many (e\&.g\&. >100) long (e\&.g\&. >1000 residue) sequences\&. Default value: Y
+.RE
+.SS "Pairwise align options"
+.PP
+\fB\-pwmatrix\fR \fIlist\fR
+.RS 4
+The scoring table which describes the similarity of each amino acid to each other\&. There are three \*(Aqin\-built\*(Aq series of weight matrices offered\&. Each consists of several matrices which work differently at different evolutionary distances\&. To see the exact details, read the documentation\&. Crudely, we store several matrices in memory, spanning the full range of amino acid distance (from almost identical sequences to highly divergent ones)\&. For very similar sequences, it is best to use a strict weight matrix which only gives a high score to identities and the most favoured conservative substitutions\&. For more divergent sequences, it is appropriate to use \*(Aqsofter\*(Aq matrices which give a high score to many other frequent substitutions\&. 1) BLOSUM (Henikoff)\&. These matrices appear to be the best available for carrying out data base similarity (homology searches)\&. The matrices used are: Blosum80, 62, 45 and 30\&. 2) PAM (Dayhoff)\&. These have been extremely widely used since the late \*(Aq70s\&. We use the PAM 120, 160, 250 and 350 matrices\&. 3) GONNET \&. These matrices were derived using almost the same procedure as the Dayhoff one (above) but are much more up to date and are based on a far larger data set\&. They appear to be more sensitive than the Dayhoff series\&. We use the GONNET 40, 80, 120, 160, 250 and 350 matrices\&. We also supply an identity matrix which gives a score of 1\&.0 to two identical amino acids and a score of zero otherwise\&. This matrix is not very useful\&. Default value: b
+.RE
+.PP
+\fB\-pwdnamatrix\fR \fIlist\fR
+.RS 4
+The scoring table which describes the scores assigned to matches and mismatches (including IUB ambiguity codes)\&. Default value: i
+.RE
+.PP
+\fB\-usermatrix\fR \fIvariable\fR
+.RS 4
+.RE
+.PP
+\fB\-pairwisedatafile\fR \fIinfile\fR
+.RS 4
+.RE
+.SS "Matrix options"
+.PP
+\fB\-matrix\fR \fIlist\fR
+.RS 4
+This gives a menu where you are offered a choice of weight matrices\&. The default for proteins is the PAM series derived by Gonnet and colleagues\&. Note, a series is used! The actual matrix that is used depends on how similar the sequences to be aligned at this alignment step are\&. Different matrices work differently at each evolutionary distance\&. There are three \*(Aqin\-built\*(Aq series of weight matrices offered\&. Each consists of several matrices which work differently at different evolutionary distances\&. To see the exact details, read the documentation\&. Crudely, we store several matrices in memory, spanning the full range of amino acid distance (from almost identical sequences to highly divergent ones)\&. For very similar sequences, it is best to use a strict weight matrix which only gives a high score to identities and the most favoured conservative substitutions\&. For more divergent sequences, it is appropriate to use \*(Aqsofter\*(Aq matrices which give a high score to many other frequent substitutions\&. 1) BLOSUM (Henikoff)\&. These matrices appear to be the best available for carrying out data base similarity (homology searches)\&. The matrices used are: Blosum80, 62, 45 and 30\&. 2) PAM (Dayhoff)\&. These have been extremely widely used since the late \*(Aq70s\&. We use the PAM 120, 160, 250 and 350 matrices\&. 3) GONNET \&. These matrices were derived using almost the same procedure as the Dayhoff one (above) but are much more up to date and are based on a far larger data set\&. They appear to be more sensitive than the Dayhoff series\&. We use the GONNET 40, 80, 120, 160, 250 and 350 matrices\&. We also supply an identity matrix which gives a score of 1\&.0 to two identical amino acids and a score of zero otherwise\&. This matrix is not very useful\&. Alternatively, you can read in your own (just one matrix, not a series)\&. Default value: b
+.RE
+.PP
+\fB\-usermamatrix\fR \fIvariable\fR
+.RS 4
+.RE
+.PP
+\fB\-dnamatrix\fR \fIlist\fR
+.RS 4
+This gives a menu where a single matrix (not a series) can be selected\&. Default value: i
+.RE
+.PP
+\fB\-umamatrix\fR \fIvariable\fR
+.RS 4
+.RE
+.PP
+\fB\-mamatrixfile\fR \fIinfile\fR
+.RS 4
+.RE
+.SS "Additional section"
+.SS "Slow align options"
+.PP
+\fB\-pwgapopen\fR \fIfloat\fR
+.RS 4
+The penalty for opening a gap in the pairwise alignments\&. Default value: 10\&.0
+.RE
+.PP
+\fB\-pwgapextend\fR \fIfloat\fR
+.RS 4
+The penalty for extending a gap by 1 residue in the pairwise alignments\&. Default value: 0\&.1
+.RE
+.SS "Fast align options"
+.PP
+\fB\-ktup\fR \fIinteger\fR
+.RS 4
+This is the size of exactly matching fragment that is used\&. INCREASE for speed (max= 2 for proteins; 4 for DNA), DECREASE for sensitivity\&. For longer sequences (e\&.g\&. >1000 residues) you may need to increase the default\&. Default value: @($(acdprotein)?1:2)
+.RE
+.PP
+\fB\-gapw\fR \fIinteger\fR
+.RS 4
+This is a penalty for each gap in the fast alignments\&. It has little affect on the speed or sensitivity except for extreme values\&. Default value: @($(acdprotein)?3:5)
+.RE
+.PP
+\fB\-topdiags\fR \fIinteger\fR
+.RS 4
+The number of k\-tuple matches on each diagonal (in an imaginary dot\-matrix plot) is calculated\&. Only the best ones (with most matches) are used in the alignment\&. This parameter specifies how many\&. Decrease for speed; increase for sensitivity\&. Default value: @($(acdprotein)?5:4)
+.RE
+.PP
+\fB\-window\fR \fIinteger\fR
+.RS 4
+This is the number of diagonals around each of the \*(Aqbest\*(Aq diagonals that will be used\&. Decrease for speed; increase for sensitivity\&. Default value: @($(acdprotein)?5:4)
+.RE
+.PP
+\fB\-nopercent\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.SS "Gap options"
+.PP
+\fB\-gapopen\fR \fIfloat\fR
+.RS 4
+The penalty for opening a gap in the alignment\&. Increasing the gap opening penalty will make gaps less frequent\&. Default value: 10\&.0
+.RE
+.PP
+\fB\-gapextend\fR \fIfloat\fR
+.RS 4
+The penalty for extending a gap by 1 residue\&. Increasing the gap extension penalty will make gaps shorter\&. Terminal gaps are not penalised\&. Default value: 5\&.0
+.RE
+.PP
+\fB\-endgaps\fR \fIboolean\fR
+.RS 4
+End gap separation: treats end gaps just like internal gaps for the purposes of avoiding gaps that are too close (set by \*(Aqgap separation distance\*(Aq)\&. If you turn this off, end gaps will be ignored for this purpose\&. This is useful when you wish to align fragments where the end gaps are not biologically meaningful\&. Default value: Y
+.RE
+.PP
+\fB\-gapdist\fR \fIinteger\fR
+.RS 4
+Gap separation distance: tries to decrease the chances of gaps being too close to each other\&. Gaps that are less than this distance apart are penalised more than other gaps\&. This does not prevent close gaps; it makes them less frequent, promoting a block\-like appearance of the alignment\&. Default value: 8
+.RE
+.PP
+\fB\-norgap\fR \fIboolean\fR
+.RS 4
+Residue specific penalties: amino acid specific gap penalties that reduce or increase the gap opening penalties at each position in the alignment or sequence\&. As an example, positions that are rich in glycine are more likely to have an adjacent gap than positions that are rich in valine\&. Default value: N
+.RE
+.PP
+\fB\-hgapres\fR \fIstring\fR
+.RS 4
+This is a set of the residues \*(Aqconsidered\*(Aq to be hydrophilic\&. It is used when introducing Hydrophilic gap penalties\&. Default value: GPSNDQEKR
+.RE
+.PP
+\fB\-nohgap\fR \fIboolean\fR
+.RS 4
+Hydrophilic gap penalties: used to increase the chances of a gap within a run (5 or more residues) of hydrophilic amino acids; these are likely to be loop or random coil regions where gaps are more common\&. The residues that are \*(Aqconsidered\*(Aq to be hydrophilic are set by \*(Aq\-hgapres\*(Aq\&. Default value: N
+.RE
+.PP
+\fB\-maxdiv\fR \fIinteger\fR
+.RS 4
+This switch, delays the alignment of the most distantly related sequences until after the most closely related sequences have been aligned\&. The setting shows the percent identity level required to delay the addition of a sequence; sequences that are less identical than this level to any other sequences will be aligned later\&. Default value: 30
+.RE
+.SS "Output section"
+.PP
+\fB\-outseq\fR \fIseqoutset\fR
+.RS 4
+.RE
+.PP
+\fB\-dendoutfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+emma is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/textvalid.1e
+++ emboss-6.4.0/debian/manpages/textvalid.1e
@@ -0,0 +1,78 @@
+'\" t
+.\"     Title: TEXTVALID
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "TEXTVALID" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+textvalid \- Check a plain text format is valid
+.SH "SYNOPSIS"
+.HP \w'\fBtextvalid\fR\ 'u
+\fBtextvalid\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR [\fB\-type\ \fR\fB\fIlist\fR\fR] \fB\-logfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBtextvalid\fR\ 'u
+\fBtextvalid\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBtextvalid\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Misc" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-infile\fR \fIinfile\fR
+.RS 4
+.RE
+.SS "Required section"
+.SS "Additional section"
+.PP
+\fB\-type\fR \fIlist\fR
+.RS 4
+If you know the type of file content then specify it using this option\&. This will help textvalid to identify and validate the file format\&.
+.RE
+.SS "Advanced section"
+.SS "Output section"
+.PP
+\fB\-logfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+textvalid is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/edamclean.1e
+++ emboss-6.4.0/debian/manpages/edamclean.1e
@@ -0,0 +1,97 @@
+'\" t
+.\"     Title: EDAMCLEAN
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "EDAMCLEAN" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+edamclean \- Validate and fix EDAM OBO ontology
+.SH "SYNOPSIS"
+.HP \w'\fBedamclean\fR\ 'u
+\fBedamclean\fR \fB\-edaminfile\ \fR\fB\fIinfile\fR\fR \fB\-taxdirectory\ \fR\fB\fIdirectory\fR\fR \fB\-mode\ \fR\fB\fIselection\fR\fR \fB\-edamoutfile\ \fR\fB\fIoutfile\fR\fR \fB\-logfile\ \fR\fB\fIoutfile\fR\fR \fB\-xmlfile\ \fR\fB\fIoutfile\fR\fR \fB\-xmloutdir\ \fR\fB\fIoutdir\fR\fR
+.HP \w'\fBedamclean\fR\ 'u
+\fBedamclean\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBedamclean\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Ontology:EDAM" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-edaminfile\fR \fIinfile\fR
+.RS 4
+Default value: /homes/jison/edam/EDAM\&.obo
+.RE
+.PP
+\fB\-taxdirectory\fR \fIdirectory\fR
+.RS 4
+.RE
+.SS "Required section"
+.PP
+\fB\-mode\fR \fIselection\fR
+.RS 4
+Default value: Report only
+.RE
+.SS "Advanced section"
+.SS "Output section"
+.PP
+\fB\-edamoutfile\fR \fIoutfile\fR
+.RS 4
+Default value: EDAM_out\&.obo
+.RE
+.PP
+\fB\-logfile\fR \fIoutfile\fR
+.RS 4
+Default value: EDAM_out\&.log
+.RE
+.PP
+\fB\-xmlfile\fR \fIoutfile\fR
+.RS 4
+Default value: EDAM_out\&.xml
+.RE
+.PP
+\fB\-xmloutdir\fR \fIoutdir\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+edamclean is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/ajtest.1e
+++ emboss-6.4.0/debian/manpages/ajtest.1e
@@ -0,0 +1,95 @@
+'\" t
+.\"     Title: AJTEST
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "AJTEST" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+ajtest \- Test file for ACD parsing
+.SH "SYNOPSIS"
+.HP \w'\fBajtest\fR\ 'u
+\fBajtest\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-bsequence\ \fR\fB\fIseqset\fR\fR \fB\-idresource\ \fR\fB\fIstring\fR\fR \fB\-taxdir\ \fR\fB\fIdirectory\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR \fB\-outseq\ \fR\fB\fIseqout\fR\fR \fB\-outfeat\ \fR\fB\fIfeatout\fR\fR \fB\-outdir\ \fR\fB\fIoutdir\fR\fR
+.HP \w'\fBajtest\fR\ 'u
+\fBajtest\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBajtest\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Test" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqall\fR
+.RS 4
+.RE
+.PP
+\fB\-bsequence\fR \fIseqset\fR
+.RS 4
+.RE
+.PP
+\fB\-idresource\fR \fIstring\fR
+.RS 4
+.RE
+.PP
+\fB\-taxdir\fR \fIdirectory\fR
+.RS 4
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.PP
+\fB\-outseq\fR \fIseqout\fR
+.RS 4
+.RE
+.PP
+\fB\-outfeat\fR \fIfeatout\fR
+.RS 4
+.RE
+.PP
+\fB\-outdir\fR \fIoutdir\fR
+.RS 4
+Default value: /tmp
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+ajtest is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/ontogetdown.1e
+++ emboss-6.4.0/debian/manpages/ontogetdown.1e
@@ -0,0 +1,77 @@
+'\" t
+.\"     Title: ONTOGETDOWN
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "ONTOGETDOWN" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+ontogetdown \- Get ontology term(s) by parent id
+.SH "SYNOPSIS"
+.HP \w'\fBontogetdown\fR\ 'u
+\fBontogetdown\fR \fB\-oboterms\ \fR\fB\fIobo\fR\fR [\fB\-obsolete\ \fR\fB\fIboolean\fR\fR] \fB\-outfile\ \fR\fB\fIoutobo\fR\fR
+.HP \w'\fBontogetdown\fR\ 'u
+\fBontogetdown\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBontogetdown\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Ontology,Data retrieval:Ontology data" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-oboterms\fR \fIobo\fR
+.RS 4
+.RE
+.SS "Additional section"
+.PP
+\fB\-obsolete\fR \fIboolean\fR
+.RS 4
+The default behaviour is to not use or return obsolete terms\&. This option if set will include all terms\&. Default value: N
+.RE
+.SS "Advanced section"
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutobo\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+ontogetdown is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/needleall.1e
+++ emboss-6.4.0/debian/manpages/needleall.1e
@@ -0,0 +1,121 @@
+'\" t
+.\"     Title: NEEDLEALL
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "NEEDLEALL" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+needleall \- Many\-to\-many pairwise alignments of two sequence sets
+.SH "SYNOPSIS"
+.HP \w'\fBneedleall\fR\ 'u
+\fBneedleall\fR \fB\-asequence\ \fR\fB\fIseqset\fR\fR \fB\-bsequence\ \fR\fB\fIseqall\fR\fR [\fB\-datafile\ \fR\fB\fImatrixf\fR\fR] \fB\-gapopen\ \fR\fB\fIfloat\fR\fR \fB\-gapextend\ \fR\fB\fIfloat\fR\fR [\fB\-endweight\ \fR\fB\fIboolean\fR\fR] [\fB\-endopen\ \fR\fB\fIfloat\fR\fR] [\fB\-endextend\ \fR\fB\fIfloat\fR\fR] [\fB\-minscore\ \fR\fB\fIfloat\fR\fR] \fB\-brief\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIalign\fR\fR [\fB\-errorfile\ \fR\fB\fIoutfile\fR\fR]
+.HP \w'\fBneedleall\fR\ 'u
+\fBneedleall\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBneedleall\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Alignment:Global" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-asequence\fR \fIseqset\fR
+.RS 4
+.RE
+.PP
+\fB\-bsequence\fR \fIseqall\fR
+.RS 4
+.RE
+.PP
+\fB\-datafile\fR \fImatrixf\fR
+.RS 4
+This is the scoring matrix file used when comparing sequences\&. By default it is the file \*(AqEBLOSUM62\*(Aq (for proteins) or the file \*(AqEDNAFULL\*(Aq (for nucleic sequences)\&. These files are found in the \*(Aqdata\*(Aq directory of the EMBOSS installation\&.
+.RE
+.SS "Required section"
+.PP
+\fB\-gapopen\fR \fIfloat\fR
+.RS 4
+The gap open penalty is the score taken away when a gap is created\&. The best value depends on the choice of comparison matrix\&. The default value assumes you are using the EBLOSUM62 matrix for protein sequences, and the EDNAFULL matrix for nucleotide sequences\&. Default value: @($(acdprotein)? 10\&.0 : 10\&.0 )
+.RE
+.PP
+\fB\-gapextend\fR \fIfloat\fR
+.RS 4
+The gap extension, penalty is added to the standard gap penalty for each base or residue in the gap\&. This is how long gaps are penalized\&. Usually you will expect a few long gaps rather than many short gaps, so the gap extension penalty should be lower than the gap penalty\&. An exception is where one or both sequences are single reads with possible sequencing errors in which case you would expect many single base gaps\&. You can get this result by setting the gap open penalty to zero (or very low) and using the gap extension penalty to control gap scoring\&. Default value: @($(acdprotein)? 0\&.5 : 0\&.5 )
+.RE
+.SS "Additional section"
+.PP
+\fB\-endweight\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-endopen\fR \fIfloat\fR
+.RS 4
+The end gap open penalty is the score taken away when an end gap is created\&. The best value depends on the choice of comparison matrix\&. The default value assumes you are using the EBLOSUM62 matrix for protein sequences, and the EDNAFULL matrix for nucleotide sequences\&. Default value: @($(acdprotein)? 10\&.0 : 10\&.0 )
+.RE
+.PP
+\fB\-endextend\fR \fIfloat\fR
+.RS 4
+The end gap extension, penalty is added to the end gap penalty for each base or residue in the end gap\&. Default value: @($(acdprotein)? 0\&.5 : 0\&.5 )
+.RE
+.PP
+\fB\-minscore\fR \fIfloat\fR
+.RS 4
+Minimum alignment score to report an alignment\&.
+.RE
+.SS "Output section"
+.PP
+\fB\-brief\fR \fIboolean\fR
+.RS 4
+Brief identity and similarity Default value: Y
+.RE
+.PP
+\fB\-outfile\fR \fIalign\fR
+.RS 4
+.RE
+.PP
+\fB\-errorfile\fR \fIoutfile\fR
+.RS 4
+Error file to be written to Default value: needleall\&.error
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+needleall is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/geecee.1e
+++ emboss-6.4.0/debian/manpages/geecee.1e
@@ -0,0 +1,70 @@
+'\" t
+.\"     Title: GEECEE
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "GEECEE" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+geecee \- Calculate fractional GC content of nucleic acid sequences
+.SH "SYNOPSIS"
+.HP \w'\fBgeecee\fR\ 'u
+\fBgeecee\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBgeecee\fR\ 'u
+\fBgeecee\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBgeecee\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:CpG Islands" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqall\fR
+.RS 4
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+geecee is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/martdatasets.1e
+++ emboss-6.4.0/debian/manpages/martdatasets.1e
@@ -0,0 +1,87 @@
+'\" t
+.\"     Title: MARTDATASETS
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "MARTDATASETS" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+martdatasets \- Return datasets from a mart from a registry
+.SH "SYNOPSIS"
+.HP \w'\fBmartdatasets\fR\ 'u
+\fBmartdatasets\fR \fB\-mart\ \fR\fB\fIstring\fR\fR \fB\-host\ \fR\fB\fIstring\fR\fR \fB\-path\ \fR\fB\fIstring\fR\fR \fB\-port\ \fR\fB\fIinteger\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBmartdatasets\fR\ 'u
+\fBmartdatasets\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBmartdatasets\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-mart\fR \fIstring\fR
+.RS 4
+Default value: ensembl
+.RE
+.SS "Advanced section"
+.PP
+\fB\-host\fR \fIstring\fR
+.RS 4
+Default value: www\&.biomart\&.org
+.RE
+.PP
+\fB\-path\fR \fIstring\fR
+.RS 4
+Default value: /biomart/martservice
+.RE
+.PP
+\fB\-port\fR \fIinteger\fR
+.RS 4
+Default value: 80
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+martdatasets is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/union.1e
+++ emboss-6.4.0/debian/manpages/union.1e
@@ -0,0 +1,90 @@
+'\" t
+.\"     Title: UNION
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "UNION" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+union \- Concatenate multiple sequences into a single sequence
+.SH "SYNOPSIS"
+.HP \w'\fBunion\fR\ 'u
+\fBunion\fR \fB\-feature\ \fR\fB\fIboolean\fR\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-source\ \fR\fB\fIboolean\fR\fR \fB\-findoverlap\ \fR\fB\fIboolean\fR\fR \fB\-outseq\ \fR\fB\fIseqout\fR\fR [\fB\-overlapfile\ \fR\fB\fIoutfile\fR\fR]
+.HP \w'\fBunion\fR\ 'u
+\fBunion\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBunion\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-feature\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-sequence\fR \fIseqall\fR
+.RS 4
+.RE
+.SS "Advanced section"
+.PP
+\fB\-source\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-findoverlap\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.SS "Output section"
+.PP
+\fB\-outseq\fR \fIseqout\fR
+.RS 4
+.RE
+.PP
+\fB\-overlapfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+union is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/feattext.1e
+++ emboss-6.4.0/debian/manpages/feattext.1e
@@ -0,0 +1,70 @@
+'\" t
+.\"     Title: FEATTEXT
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "FEATTEXT" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+feattext \- Return a feature table original text
+.SH "SYNOPSIS"
+.HP \w'\fBfeattext\fR\ 'u
+\fBfeattext\fR \fB\-features\ \fR\fB\fIfeatures\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBfeattext\fR\ 'u
+\fBfeattext\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBfeattext\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-features\fR \fIfeatures\fR
+.RS 4
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+feattext is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/digest.1e
+++ emboss-6.4.0/debian/manpages/digest.1e
@@ -0,0 +1,112 @@
+'\" t
+.\"     Title: DIGEST
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "DIGEST" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+digest \- Reports on protein proteolytic enzyme or reagent cleavage sites
+.SH "SYNOPSIS"
+.HP \w'\fBdigest\fR\ 'u
+\fBdigest\fR \fB\-seqall\ \fR\fB\fIseqall\fR\fR \fB\-mwdata\ \fR\fB\fIdatafile\fR\fR \fB\-menu\ \fR\fB\fIlist\fR\fR \fB\-mono\ \fR\fB\fIboolean\fR\fR \fB\-unfavoured\ \fR\fB\fIboolean\fR\fR \fB\-ragging\ \fR\fB\fIboolean\fR\fR \fB\-termini\ \fR\fB\fIlist\fR\fR \fB\-overlap\ \fR\fB\fIboolean\fR\fR \fB\-allpartials\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIreport\fR\fR
+.HP \w'\fBdigest\fR\ 'u
+\fBdigest\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBdigest\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Protein:Motifs" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-seqall\fR \fIseqall\fR
+.RS 4
+.RE
+.PP
+\fB\-mwdata\fR \fIdatafile\fR
+.RS 4
+Molecular weight data for amino acids Default value: Emolwt\&.dat
+.RE
+.SS "Required section"
+.PP
+\fB\-menu\fR \fIlist\fR
+.RS 4
+Default value: 1
+.RE
+.PP
+\fB\-mono\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.SS "Advanced section"
+.PP
+\fB\-unfavoured\fR \fIboolean\fR
+.RS 4
+Trypsin will not normally cut after \*(AqKR\*(Aq if they are followed by any of \*(AqKRIFLP\*(Aq\&. Lys\-C will not normally cut after \*(AqK\*(Aq if it is followed by \*(AqP\*(Aq\&. Arg\-C will not normally cut after \*(AqR\*(Aq if it is followed by \*(AqP\*(Aq\&. V8\-bicarb will not normally cut after \*(AqE\*(Aq if it is followed by any of \*(AqKREP\*(Aq\&. V8\-phosph will not normally cut after \*(AqDE\*(Aq if they are followed by \*(AqP\*(Aq\&. Chymotrypsin will not normally cut after \*(AqFYWLM\*(Aq if they are followed by \*(AqP\*(Aq\&. Specifying unfavoured shows these unfavoured cuts as well as the favoured ones\&.
+.RE
+.PP
+\fB\-ragging\fR \fIboolean\fR
+.RS 4
+Allows semi\-specific and non\-specific digestion\&. This option is particularly useful for generating lists of peptide sequences for protein identification using mass\-spectrometry\&.
+.RE
+.PP
+\fB\-termini\fR \fIlist\fR
+.RS 4
+Default value: 1
+.RE
+.SS "Output section"
+.PP
+\fB\-overlap\fR \fIboolean\fR
+.RS 4
+Used for partial digestion\&. Shows all cuts from favoured cut sites plus 1\&.\&.3, 2\&.\&.4, 3\&.\&.5 etc but not (e\&.g\&.) 2\&.\&.5\&. Overlaps are therefore fragments with exactly one potential cut site within it\&.
+.RE
+.PP
+\fB\-allpartials\fR \fIboolean\fR
+.RS 4
+As for overlap but fragments containing more than one potential cut site are included\&.
+.RE
+.PP
+\fB\-outfile\fR \fIreport\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+digest is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/marscan.1e
+++ emboss-6.4.0/debian/manpages/marscan.1e
@@ -0,0 +1,71 @@
+'\" t
+.\"     Title: MARSCAN
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "MARSCAN" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+marscan \- Finds matrix/scaffold recognition (MRS) signatures in DNA sequences
+.SH "SYNOPSIS"
+.HP \w'\fBmarscan\fR\ 'u
+\fBmarscan\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-outfile\ \fR\fB\fIreport\fR\fR
+.HP \w'\fBmarscan\fR\ 'u
+\fBmarscan\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBmarscan\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Gene finding,Nucleic:Functional sites,Nucleic:Transcription" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqall\fR
+.RS 4
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIreport\fR
+.RS 4
+File for output of MAR/SAR recognition signature (MRS) regions\&. This contains details of the MRS in normal GFF format\&. The MRS consists of two recognition sites, one of 8 bp and one of 16 bp on either sense strand of the genomic DNA, within 200 bp of each other\&.
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+marscan is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/cachedas.1e
+++ emboss-6.4.0/debian/manpages/cachedas.1e
@@ -0,0 +1,97 @@
+'\" t
+.\"     Title: CACHEDAS
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "CACHEDAS" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+cachedas \- Generates server cache file for DAS servers or for the DAS registry
+.SH "SYNOPSIS"
+.HP \w'\fBcachedas\fR\ 'u
+\fBcachedas\fR [\fB\-sequencesourcesonly\ \fR\fB\fIboolean\fR\fR] \fB\-host\ \fR\fB\fIstring\fR\fR \fB\-path\ \fR\fB\fIstring\fR\fR \fB\-port\ \fR\fB\fIinteger\fR\fR \fB\-servername\ \fR\fB\fIstring\fR\fR [\fB\-outfile\ \fR\fB\fIoutfile\fR\fR] \fB\-cachefile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBcachedas\fR\ 'u
+\fBcachedas\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBcachedas\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Data resources" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequencesourcesonly\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-host\fR \fIstring\fR
+.RS 4
+Default value: www\&.dasregistry\&.org
+.RE
+.PP
+\fB\-path\fR \fIstring\fR
+.RS 4
+Default value: /das
+.RE
+.PP
+\fB\-port\fR \fIinteger\fR
+.RS 4
+Default value: 80
+.RE
+.PP
+\fB\-servername\fR \fIstring\fR
+.RS 4
+Default value: das
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+Default value: stdout
+.RE
+.PP
+\fB\-cachefile\fR \fIoutfile\fR
+.RS 4
+Default value: server\&.$(servername)
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+cachedas is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/domtesta.1e
+++ emboss-6.4.0/debian/manpages/domtesta.1e
@@ -0,0 +1,70 @@
+'\" t
+.\"     Title: DOMTESTA
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "DOMTESTA" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+domtesta \- Reads an XML file into the DOM and writes it back out
+.SH "SYNOPSIS"
+.HP \w'\fBdomtesta\fR\ 'u
+\fBdomtesta\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBdomtesta\fR\ 'u
+\fBdomtesta\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBdomtesta\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-infile\fR \fIinfile\fR
+.RS 4
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+domtesta is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/eprimer3.1e
+++ emboss-6.4.0/debian/manpages/eprimer3.1e
@@ -0,0 +1,365 @@
+'\" t
+.\"     Title: EPRIMER3
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "EPRIMER3" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+eprimer3 \- Picks PCR primers and hybridization oligos
+.SH "SYNOPSIS"
+.HP \w'\fBeprimer3\fR\ 'u
+\fBeprimer3\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR [\fB\-primer\ \fR\fB\fItoggle\fR\fR] \fB\-task\ \fR\fB\fIlist\fR\fR [\fB\-hybridprobe\ \fR\fB\fItoggle\fR\fR] \fB\-mishyblibraryfile\ \fR\fB\fIinfile\fR\fR \fB\-mispriminglibraryfile\ \fR\fB\fIinfile\fR\fR [\fB\-numreturn\ \fR\fB\fIinteger\fR\fR] [\fB\-includedregion\ \fR\fB\fIrange\fR\fR] [\fB\-targetregion\ \fR\fB\fIrange\fR\fR] [\fB\-excludedregion\ \fR\fB\fIrange\fR\fR] [\fB\-forwardinput\ \fR\fB\fIstring\fR\fR] [\fB\-reverseinput\ \fR\fB\fIstring\fR\fR] \fB\-gcclamp\ \fR\fB\fIinteger\fR\fR \fB\-osize\ \fR\fB\fIinteger\fR\fR \fB\-minsize\ \fR\fB\fIinteger\fR\fR \fB\-maxsize\ \fR\fB\fIinteger\fR\fR \fB\-otm\ \fR\fB\fIfloat\fR\fR \fB\-mintm\ \fR\fB\fIfloat\fR\fR \fB\-maxtm\ \fR\fB\fIfloat\fR\fR \fB\-maxdifftm\ \fR\fB\fIfloat\fR\fR \fB\-ogcpercent\ \fR\fB\fIfloat\fR\fR \fB\-mingc\ \fR\fB\fIfloat\fR\fR \fB\-maxgc\ \fR\fB\fIfloat\fR\fR \fB\-saltconc\ \fR\fB\fIfloat\fR\fR \fB\-dnaconc\ \fR\fB\fIfloat\fR\fR \fB\-maxpolyx\ \fR\fB\fIinteger\fR\fR \fB\-psizeopt\ \fR\fB\fIinteger\fR\fR \fB\-prange\ \fR\fB\fIrange\fR\fR \fB\-ptmopt\ \fR\fB\fIfloat\fR\fR \fB\-ptmmin\ \fR\fB\fIfloat\fR\fR \fB\-ptmmax\ \fR\fB\fIfloat\fR\fR \fB\-oexcludedregion\ \fR\fB\fIrange\fR\fR \fB\-oligoinput\ \fR\fB\fIstring\fR\fR \fB\-osizeopt\ \fR\fB\fIinteger\fR\fR \fB\-ominsize\ \fR\fB\fIinteger\fR\fR \fB\-omaxsize\ \fR\fB\fIinteger\fR\fR \fB\-otmopt\ \fR\fB\fIfloat\fR\fR \fB\-otmmin\ \fR\fB\fIfloat\fR\fR \fB\-otmmax\ \fR\fB\fIfloat\fR\fR \fB\-ogcopt\ \fR\fB\fIfloat\fR\fR \fB\-ogcmin\ \fR\fB\fIfloat\fR\fR \fB\-ogcmax\ \fR\fB\fIfloat\fR\fR \fB\-osaltconc\ \fR\fB\fIfloat\fR\fR \fB\-odnaconc\ \fR\fB\fIfloat\fR\fR \fB\-oanyself\ \fR\fB\fIfloat\fR\fR \fB\-oendself\ \fR\fB\fIfloat\fR\fR \fB\-opolyxmax\ \fR\fB\fIinteger\fR\fR \fB\-omishybmax\ \fR\fB\fIfloat\fR\fR \fB\-explainflag\ \fR\fB\fIboolean\fR\fR \fB\-fileflag\ \fR\fB\fIboolean\fR\fR \fB\-firstbaseindex\ \fR\fB\fIinteger\fR\fR \fB\-pickanyway\ \fR\fB\fIboolean\fR\fR \fB\-maxmispriming\ \fR\fB\fIfloat\fR\fR \fB\-pairmaxmispriming\ \fR\fB\fIfloat\fR\fR \fB\-numnsaccepted\ \fR\fB\fIinteger\fR\fR \fB\-selfany\ \fR\fB\fIfloat\fR\fR \fB\-selfend\ \fR\fB\fIfloat\fR\fR \fB\-maxendstability\ \fR\fB\fIfloat\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBeprimer3\fR\ 'u
+\fBeprimer3\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBeprimer3\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Primers" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqall\fR
+.RS 4
+The sequence from which to choose primers\&. The sequence must be presented 5\*(Aq to 3\*(Aq
+.RE
+.PP
+\fB\-primer\fR \fItoggle\fR
+.RS 4
+Tell EPrimer3 to pick primer(s) Default value: Y
+.RE
+.PP
+\fB\-task\fR \fIlist\fR
+.RS 4
+Tell EPrimer3 what task to perform\&. Legal values are 1: \*(AqPick PCR primers\*(Aq, 2: \*(AqPick forward primer only\*(Aq, 3: \*(AqPick reverse primer only\*(Aq, 4: \*(AqNo primers needed\*(Aq\&. Default value: 1
+.RE
+.PP
+\fB\-hybridprobe\fR \fItoggle\fR
+.RS 4
+An \*(Aqinternal oligo\*(Aq is intended to be used as a hybridization probe (hyb probe) to detect the PCR product after amplification\&. Default value: N
+.RE
+.PP
+\fB\-mishyblibraryfile\fR \fIinfile\fR
+.RS 4
+Similar to MISPRIMING\-LIBRARY, except that the event we seek to avoid is hybridization of the internal oligo to sequences in this library rather than priming from them\&. The file must be in (a slightly restricted) FASTA format (W\&. B\&. Pearson and D\&.J\&. Lipman, PNAS 85:8 pp 2444\-2448 [1988]); we briefly discuss the organization of this file below\&. If this parameter is specified then EPrimer3 locally aligns each candidate oligo against each library sequence and rejects those primers for which the local alignment score times a specified weight (see below) exceeds INTERNAL\-OLIGO\-MAX\-MISHYB\&. (The maximum value of the weight is arbitrarily set to 12\&.0\&.) Each sequence entry in the FASTA\-format file must begin with an \*(Aqid line\*(Aq that starts with \*(Aq>\*(Aq\&. The contents of the id line is \*(Aqslightly restricted\*(Aq in that EPrimer3 parses everything after any optional asterisk (\*(Aq*\*(Aq) as a floating point number to use as the weight mentioned above\&. If the id line contains no asterisk then the weight defaults to 1\&.0\&. The alignment scoring system used is the same as for calculating complementarity among oligos (e\&.g\&. SELF\-ANY)\&. The remainder of an entry contains the sequence as lines following the id line up until a line starting with \*(Aq>\*(Aq or the end of the file\&. Whitespace and newlines are ignored\&. Characters \*(AqA\*(Aq, \*(AqT\*(Aq, \*(AqG\*(Aq, \*(AqC\*(Aq, \*(Aqa\*(Aq, \*(Aqt\*(Aq, \*(Aqg\*(Aq, \*(Aqc\*(Aq are retained and any other character is converted to \*(AqN\*(Aq (with the consequence that any IUB / IUPAC codes for ambiguous bases are converted to \*(AqN\*(Aq)\&. There are no restrictions on line length\&. An empty value for this parameter indicates that no library should be used\&.
+.RE
+.PP
+\fB\-mispriminglibraryfile\fR \fIinfile\fR
+.RS 4
+The name of a file containing a nucleotide sequence library of sequences to avoid amplifying (for example repetitive sequences, or possibly the sequences of genes in a gene family that should not be amplified\&.) The file must be in (a slightly restricted) FASTA format (W\&. B\&. Pearson and D\&.J\&. Lipman, PNAS 85:8 pp 2444\-2448 [1988]); we briefly discuss the organization of this file below\&. If this parameter is specified then EPrimer3 locally aligns each candidate primer against each library sequence and rejects those primers for which the local alignment score times a specified weight (see below) exceeds MAX\-MISPRIMING\&. (The maximum value of the weight is arbitrarily set to 100\&.0\&.) Each sequence entry in the FASTA\-format file must begin with an \*(Aqid line\*(Aq that starts with \*(Aq>\*(Aq\&. The contents of the id line is \*(Aqslightly restricted\*(Aq in that EPrimer3 parses everything after any optional asterisk (\*(Aq*\*(Aq) as a floating point number to use as the weight mentioned above\&. If the id line contains no asterisk then the weight defaults to 1\&.0\&. The alignment scoring system used is the same as for calculating complementarity among oligos (e\&.g\&. SELF\-ANY)\&. The remainder of an entry contains the sequence as lines following the id line up until a line starting with \*(Aq>\*(Aq or the end of the file\&. Whitespace and newlines are ignored\&. Characters \*(AqA\*(Aq, \*(AqT\*(Aq, \*(AqG\*(Aq, \*(AqC\*(Aq, \*(Aqa\*(Aq, \*(Aqt\*(Aq, \*(Aqg\*(Aq, \*(Aqc\*(Aq are retained and any other character is converted to \*(AqN\*(Aq (with the consequence that any IUB / IUPAC codes for ambiguous bases are converted to \*(AqN\*(Aq)\&. There are no restrictions on line length\&. An empty value for this parameter indicates that no repeat library should be used\&.
+.RE
+.SS "Additional section"
+.SS "Program options"
+.PP
+\fB\-numreturn\fR \fIinteger\fR
+.RS 4
+The maximum number of primer pairs to return\&. Primer pairs returned are sorted by their \*(Aqquality\*(Aq, in other words by the value of the objective function (where a lower number indicates a better primer pair)\&. Caution: setting this parameter to a large value will increase running time\&. Default value: 5
+.RE
+.SS "Sequence options"
+.PP
+\fB\-includedregion\fR \fIrange\fR
+.RS 4
+A sub\-region of the given sequence in which to pick primers\&. For example, often the first dozen or so bases of a sequence are vector, and should be excluded from consideration\&. The value for this parameter has the form (start),(end) where (start) is the index of the first base to consider, and (end) is the last in the primer\-picking region\&.
+.RE
+.PP
+\fB\-targetregion\fR \fIrange\fR
+.RS 4
+If one or more Targets is specified then a legal primer pair must flank at least one of them\&. A Target might be a simple sequence repeat site (for example a CA repeat) or a single\-base\-pair polymorphism\&. The value should be a space\-separated list of (start),(end) pairs where (start) is the index of the first base of a Target, and (end) is the last E\&.g\&. 50,51 requires primers to surround the 2 bases at positions 50 and 51\&.
+.RE
+.PP
+\fB\-excludedregion\fR \fIrange\fR
+.RS 4
+Primer oligos may not overlap any region specified in this tag\&. The associated value must be a space\-separated list of (start),(end) pairs where (start) is the index of the first base of the excluded region, and and (end) is the last\&. This tag is useful for tasks such as excluding regions of low sequence quality or for excluding regions containing repetitive elements such as ALUs or LINEs\&. E\&.g\&. 401,407 68,70 forbids selection of primers in the 7 bases starting at 401 and the 3 bases at 68\&.
+.RE
+.PP
+\fB\-forwardinput\fR \fIstring\fR
+.RS 4
+The sequence of a forward primer to check and around which to design reverse primers and optional internal oligos\&. Must be a substring of SEQUENCE\&.
+.RE
+.PP
+\fB\-reverseinput\fR \fIstring\fR
+.RS 4
+The sequence of a reverse primer to check and around which to design forward primers and optional internal oligos\&. Must be a substring of the reverse strand of SEQUENCE\&.
+.RE
+.SS "Primer options"
+.PP
+\fB\-gcclamp\fR \fIinteger\fR
+.RS 4
+Require the specified number of consecutive Gs and Cs at the 3\*(Aq end of both the forward and reverse primer\&. (This parameter has no effect on the internal oligo if one is requested\&.)
+.RE
+.PP
+\fB\-osize\fR \fIinteger\fR
+.RS 4
+Optimum length (in bases) of a primer oligo\&. EPrimer3 will attempt to pick primers close to this length\&. Default value: 20
+.RE
+.PP
+\fB\-minsize\fR \fIinteger\fR
+.RS 4
+Minimum acceptable length of a primer\&. Must be greater than 0 and less than or equal to MAX\-SIZE\&. Default value: 18
+.RE
+.PP
+\fB\-maxsize\fR \fIinteger\fR
+.RS 4
+Maximum acceptable length (in bases) of a primer\&. Currently this parameter cannot be larger than 35\&. This limit is governed by the maximum oligo size for which EPrimer3\*(Aqs melting\-temperature is valid\&. Default value: 27
+.RE
+.PP
+\fB\-otm\fR \fIfloat\fR
+.RS 4
+Optimum melting temperature(Celsius) for a primer oligo\&. EPrimer3 will try to pick primers with melting temperatures are close to this temperature\&. The oligo melting temperature formula in EPrimer3 is that given in Rychlik, Spencer and Rhoads, Nucleic Acids Research, vol 18, num 21, pp 6409\-6412 and Breslauer, Frank, Bloecker and Marky, Proc\&. Natl\&. Acad\&. Sci\&. USA, vol 83, pp 3746\-3750\&. Please refer to the former paper for background discussion\&. Default value: 60\&.0
+.RE
+.PP
+\fB\-mintm\fR \fIfloat\fR
+.RS 4
+Minimum acceptable melting temperature(Celsius) for a primer oligo\&. Default value: 57\&.0
+.RE
+.PP
+\fB\-maxtm\fR \fIfloat\fR
+.RS 4
+Maximum acceptable melting temperature(Celsius) for a primer oligo\&. Default value: 63\&.0
+.RE
+.PP
+\fB\-maxdifftm\fR \fIfloat\fR
+.RS 4
+Maximum acceptable (unsigned) difference between the melting temperatures of the forward and reverse primers\&. Default value: 100\&.0
+.RE
+.PP
+\fB\-ogcpercent\fR \fIfloat\fR
+.RS 4
+Primer optimum GC percent\&. Default value: 50\&.0
+.RE
+.PP
+\fB\-mingc\fR \fIfloat\fR
+.RS 4
+Minimum allowable percentage of Gs and Cs in any primer\&. Default value: 20\&.0
+.RE
+.PP
+\fB\-maxgc\fR \fIfloat\fR
+.RS 4
+Maximum allowable percentage of Gs and Cs in any primer generated by Primer\&. Default value: 80\&.0
+.RE
+.PP
+\fB\-saltconc\fR \fIfloat\fR
+.RS 4
+The millimolar concentration of salt (usually KCl) in the PCR\&. EPrimer3 uses this argument to calculate oligo melting temperatures\&. Default value: 50\&.0
+.RE
+.PP
+\fB\-dnaconc\fR \fIfloat\fR
+.RS 4
+The nanomolar concentration of annealing oligos in the PCR\&. EPrimer3 uses this argument to calculate oligo melting temperatures\&. The default (50nM) works well with the standard protocol used at the Whitehead/MIT Center for Genome Research\-\-0\&.5 microliters of 20 micromolar concentration for each primer oligo in a 20 microliter reaction with 10 nanograms template, 0\&.025 units/microliter Taq polymerase in 0\&.1 mM each dNTP, 1\&.5mM MgCl2, 50mM KCl, 10mM Tris\-HCL (pH 9\&.3) using 35 cycles with an annealing temperature of 56 degrees Celsius\&. This parameter corresponds to \*(Aqc\*(Aq in Rychlik, Spencer and Rhoads\*(Aq equation (ii) (Nucleic Acids Research, vol 18, num 21) where a suitable value (for a lower initial concentration of template) is \*(Aqempirically determined\*(Aq\&. The value of this parameter is less than the actual concentration of oligos in the reaction because it is the concentration of annealing oligos, which in turn depends on the amount of template (including PCR product) in a given cycle\&. This concentration increases a great deal during a PCR; fortunately PCR seems quite robust for a variety of oligo melting temperatures\&. See ADVICE FOR PICKING PRIMERS\&. Default value: 50\&.0
+.RE
+.PP
+\fB\-maxpolyx\fR \fIinteger\fR
+.RS 4
+The maximum allowable length of a mononucleotide repeat in a primer, for example AAAAAA\&. Default value: 5
+.RE
+.SS "Product options"
+.PP
+\fB\-psizeopt\fR \fIinteger\fR
+.RS 4
+The optimum size for the PCR product\&. 0 indicates that there is no optimum product size\&. Default value: 200
+.RE
+.PP
+\fB\-prange\fR \fIrange\fR
+.RS 4
+The associated values specify the lengths of the product that the user wants the primers to create, and is a space separated list of elements of the form (x)\-(y) where an (x)\-(y) pair is a legal range of lengths for the product\&. For example, if one wants PCR products to be between 100 to 150 bases (inclusive) then one would set this parameter to 100\-150\&. If one desires PCR products in either the range from 100 to 150 bases or in the range from 200 to 250 bases then one would set this parameter to 100\-150 200\-250\&. EPrimer3 favors ranges to the left side of the parameter string\&. EPrimer3 will return legal primers pairs in the first range regardless the value of the objective function for these pairs\&. Only if there are an insufficient number of primers in the first range will EPrimer3 return primers in a subsequent range\&. Default value: 100\-300
+.RE
+.PP
+\fB\-ptmopt\fR \fIfloat\fR
+.RS 4
+The optimum melting temperature for the PCR product\&. 0 indicates that there is no optimum temperature\&. Default value: 0\&.0
+.RE
+.PP
+\fB\-ptmmin\fR \fIfloat\fR
+.RS 4
+The minimum allowed melting temperature of the amplicon\&. Please see the documentation on the maximum melting temperature of the product for details\&. Default value: \-1000000\&.0
+.RE
+.PP
+\fB\-ptmmax\fR \fIfloat\fR
+.RS 4
+The maximum allowed melting temperature of the amplicon\&. Product Tm is calculated using the formula from Bolton and McCarthy, PNAS 84:1390 (1962) as presented in Sambrook, Fritsch and Maniatis, Molecular Cloning, p 11\&.46 (1989, CSHL Press)\&. Tm = 81\&.5 + 16\&.6(log10([Na+])) + \&.41*(%GC) \- 600/length Where [Na+} is the molar sodium concentration, (%GC) is the percent of Gs and Cs in the sequence, and length is the length of the sequence\&. A similar formula is used by the prime primer selection program in GCG, which instead uses 675\&.0/length in the last term (after F\&. Baldino, Jr, M\&.\-F\&. Chesselet, and M\&.E\&. Lewis, Methods in Enzymology 168:766 (1989) eqn (1) on page 766 without the mismatch and formamide terms)\&. The formulas here and in Baldino et al\&. assume Na+ rather than K+\&. According to J\&.G\&. Wetmur, Critical Reviews in BioChem\&. and Mol\&. Bio\&. 26:227 (1991) 50 mM K+ should be equivalent in these formulae to \&.2 M Na+\&. EPrimer3 uses the same salt concentration value for calculating both the primer melting temperature and the oligo melting temperature\&. If you are planning to use the PCR product for hybridization later this behavior will not give you the Tm under hybridization conditions\&. Default value: 1000000\&.0
+.RE
+.SS "Internal oligo input"
+.PP
+\fB\-oexcludedregion\fR \fIrange\fR
+.RS 4
+Middle oligos may not overlap any region specified by this tag\&. The associated value must be a space\-separated list of (start),(end) pairs, where (start) is the index of the first base of an excluded region, and (end) is the last\&. Often one would make Target regions excluded regions for internal oligos\&.
+.RE
+.PP
+\fB\-oligoinput\fR \fIstring\fR
+.RS 4
+The sequence of an internal oligo to check and around which to design forward and reverse primers\&. Must be a substring of SEQUENCE\&.
+.RE
+.SS "Internal oligo options"
+.PP
+\fB\-osizeopt\fR \fIinteger\fR
+.RS 4
+Optimum length (in bases) of an internal oligo\&. EPrimer3 will attempt to pick primers close to this length\&. Default value: 20
+.RE
+.PP
+\fB\-ominsize\fR \fIinteger\fR
+.RS 4
+Minimum acceptable length of an internal oligo\&. Must be greater than 0 and less than or equal to INTERNAL\-OLIGO\-MAX\-SIZE\&. Default value: 18
+.RE
+.PP
+\fB\-omaxsize\fR \fIinteger\fR
+.RS 4
+Maximum acceptable length (in bases) of an internal oligo\&. Currently this parameter cannot be larger than 35\&. This limit is governed by maximum oligo size for which EPrimer3\*(Aqs melting\-temperature is valid\&. Default value: 27
+.RE
+.PP
+\fB\-otmopt\fR \fIfloat\fR
+.RS 4
+Optimum melting temperature (Celsius) for an internal oligo\&. EPrimer3 will try to pick oligos with melting temperatures that are close to this temperature\&. The oligo melting temperature formula in EPrimer3 is that given in Rychlik, Spencer and Rhoads, Nucleic Acids Research, vol 18, num 21, pp 6409\-6412 and Breslauer, Frank, Bloecker and Marky, Proc\&. Natl\&. Acad\&. Sci\&. USA, vol 83, pp 3746\-3750\&. Please refer to the former paper for background discussion\&. Default value: 60\&.0
+.RE
+.PP
+\fB\-otmmin\fR \fIfloat\fR
+.RS 4
+Minimum acceptable melting temperature(Celsius) for an internal oligo\&. Default value: 57\&.0
+.RE
+.PP
+\fB\-otmmax\fR \fIfloat\fR
+.RS 4
+Maximum acceptable melting temperature (Celsius) for an internal oligo\&. Default value: 63\&.0
+.RE
+.PP
+\fB\-ogcopt\fR \fIfloat\fR
+.RS 4
+Internal oligo optimum GC percent\&. Default value: 50\&.0
+.RE
+.PP
+\fB\-ogcmin\fR \fIfloat\fR
+.RS 4
+Minimum allowable percentage of Gs and Cs in an internal oligo\&. Default value: 20\&.0
+.RE
+.PP
+\fB\-ogcmax\fR \fIfloat\fR
+.RS 4
+Maximum allowable percentage of Gs and Cs in any internal oligo generated by Primer\&. Default value: 80\&.0
+.RE
+.PP
+\fB\-osaltconc\fR \fIfloat\fR
+.RS 4
+The millimolar concentration of salt (usually KCl) in the hybridization\&. EPrimer3 uses this argument to calculate internal oligo melting temperatures\&. Default value: 50\&.0
+.RE
+.PP
+\fB\-odnaconc\fR \fIfloat\fR
+.RS 4
+The nanomolar concentration of annealing internal oligo in the hybridization\&. Default value: 50\&.0
+.RE
+.PP
+\fB\-oanyself\fR \fIfloat\fR
+.RS 4
+The maximum allowable local alignment score when testing an internal oligo for (local) self\-complementarity\&. Local self\-complementarity is taken to predict the tendency of oligos to anneal to themselves The scoring system gives 1\&.00 for complementary bases, \-0\&.25 for a match of any base (or N) with an N, \-1\&.00 for a mismatch, and \-2\&.00 for a gap\&. Only single\-base\-pair gaps are allowed\&. For example, the alignment 5\*(Aq ATCGNA 3\*(Aq || | | 3\*(Aq TA\-CGT 5\*(Aq is allowed (and yields a score of 1\&.75), but the alignment 5\*(Aq ATCCGNA 3\*(Aq || | | 3\*(Aq TA\-\-CGT 5\*(Aq is not considered\&. Scores are non\-negative, and a score of 0\&.00 indicates that there is no reasonable local alignment between two oligos\&. Default value: 12\&.00
+.RE
+.PP
+\fB\-oendself\fR \fIfloat\fR
+.RS 4
+The maximum allowable 3\*(Aq\-anchored global alignment score when testing a single oligo for self\-complementarity\&. The scoring system is as for the Maximum Complementarity argument\&. In the examples above the scores are 7\&.00 and 6\&.00 respectively\&. Scores are non\-negative, and a score of 0\&.00 indicates that there is no reasonable 3\*(Aq\-anchored global alignment between two oligos\&. In order to estimate 3\*(Aq\-anchored global alignments for candidate oligos, Primer assumes that the sequence from which to choose oligos is presented 5\*(Aq to 3\*(Aq\&. INTERNAL\-OLIGO\-SELF\-END is meaningless when applied to internal oligos used for hybridization\-based detection, since primer\-dimer will not occur\&. We recommend that INTERNAL\-OLIGO\-SELF\-END be set at least as high as INTERNAL\-OLIGO\-SELF\-ANY\&. Default value: 12\&.00
+.RE
+.PP
+\fB\-opolyxmax\fR \fIinteger\fR
+.RS 4
+The maximum allowable length of an internal oligo mononucleotide repeat, for example AAAAAA\&. Default value: 5
+.RE
+.PP
+\fB\-omishybmax\fR \fIfloat\fR
+.RS 4
+Similar to MAX\-MISPRIMING except that this parameter applies to the similarity of candidate internal oligos to the library specified in INTERNAL\-OLIGO\-MISHYB\-LIBRARY\&. Default value: 12\&.0
+.RE
+.SS "Advanced section"
+.PP
+\fB\-explainflag\fR \fIboolean\fR
+.RS 4
+If this flag is true, produce LEFT\-EXPLAIN, RIGHT\-EXPLAIN, and INTERNAL\-OLIGO\-EXPLAIN output tags, which are intended to provide information on the number of oligos and primer pairs that EPrimer3 examined, and statistics on the number discarded for various reasons\&. Default value: N
+.RE
+.PP
+\fB\-fileflag\fR \fIboolean\fR
+.RS 4
+If the associated value is true, then EPrimer3 creates two output files for each input SEQUENCE\&. File (sequence\-id)\&.for lists all acceptable forward primers for (sequence\-id), and (sequence\-id)\&.rev lists all acceptable reverse primers for (sequence\-id), where (sequence\-id) is the value of the SEQUENCE\-ID tag (which must be supplied)\&. In addition, if the input tag TASK is 1 or 4, EPrimer3 produces a file (sequence\-id)\&.int, which lists all acceptable internal oligos\&. Default value: N
+.RE
+.PP
+\fB\-firstbaseindex\fR \fIinteger\fR
+.RS 4
+This parameter is the index of the first base in the input sequence\&. For input and output using 1\-based indexing (such as that used in GenBank and to which many users are accustomed) set this parameter to 1\&. For input and output using 0\-based indexing set this parameter to 0\&. (This parameter also affects the indexes in the contents of the files produced when the primer file flag is set\&.) Default value: 1
+.RE
+.PP
+\fB\-pickanyway\fR \fIboolean\fR
+.RS 4
+If true pick a primer pair even if LEFT\-INPUT, RIGHT\-INPUT, or INTERNAL\-OLIGO\-INPUT violates specific constraints\&. Default value: N
+.RE
+.PP
+\fB\-maxmispriming\fR \fIfloat\fR
+.RS 4
+The maximum allowed weighted similarity with any sequence in MISPRIMING\-LIBRARY\&. Default value: 12\&.00
+.RE
+.PP
+\fB\-pairmaxmispriming\fR \fIfloat\fR
+.RS 4
+The maximum allowed sum of weighted similarities of a primer pair (one similarity for each primer) with any single sequence in MISPRIMING\-LIBRARY\&. Default value: 24\&.00
+.RE
+.PP
+\fB\-numnsaccepted\fR \fIinteger\fR
+.RS 4
+Maximum number of unknown bases (N) allowable in any primer\&.
+.RE
+.PP
+\fB\-selfany\fR \fIfloat\fR
+.RS 4
+The maximum allowable local alignment score when testing a single primer for (local) self\-complementarity and the maximum allowable local alignment score when testing for complementarity between forward and reverse primers\&. Local self\-complementarity is taken to predict the tendency of primers to anneal to each other without necessarily causing self\-priming in the PCR\&. The scoring system gives 1\&.00 for complementary bases, \-0\&.25 for a match of any base (or N) with an N, \-1\&.00 for a mismatch, and \-2\&.00 for a gap\&. Only single\-base\-pair gaps are allowed\&. For example, the alignment 5\*(Aq ATCGNA 3\*(Aq \&.\&.\&.|| | | 3\*(Aq TA\-CGT 5\*(Aq is allowed (and yields a score of 1\&.75), but the alignment 5\*(Aq ATCCGNA 3\*(Aq \&.\&.\&.|| | | 3\*(Aq TA\-\-CGT 5\*(Aq is not considered\&. Scores are non\-negative, and a score of 0\&.00 indicates that there is no reasonable local alignment between two oligos\&. Default value: 8\&.00
+.RE
+.PP
+\fB\-selfend\fR \fIfloat\fR
+.RS 4
+The maximum allowable 3\*(Aq\-anchored global alignment score when testing a single primer for self\-complementarity, and the maximum allowable 3\*(Aq\-anchored global alignment score when testing for complementarity between forward and reverse primers\&. The 3\*(Aq\-anchored global alignment score is taken to predict the likelihood of PCR\-priming primer\-dimers, for example 5\*(Aq ATGCCCTAGCTTCCGGATG 3\*(Aq \&.\&.\&.\&.\&.\&.\&.\&.\&.\&.\&.\&.\&.||| ||||| \&.\&.\&.\&.\&.\&.\&.\&.\&.\&.3\*(Aq AAGTCCTACATTTAGCCTAGT 5\*(Aq or 5\*(Aq AGGCTATGGGCCTCGCGA 3\*(Aq \&.\&.\&.\&.\&.\&.\&.\&.\&.\&.\&.\&.\&.\&.\&.|||||| \&.\&.\&.\&.\&.\&.\&.\&.\&.\&.\&.\&.3\*(Aq AGCGCTCCGGGTATCGGA 5\*(Aq The scoring system is as for the Maximum Complementarity argument\&. In the examples above the scores are 7\&.00 and 6\&.00 respectively\&. Scores are non\-negative, and a score of 0\&.00 indicates that there is no reasonable 3\*(Aq\-anchored global alignment between two oligos\&. In order to estimate 3\*(Aq\-anchored global alignments for candidate primers and primer pairs, Primer assumes that the sequence from which to choose primers is presented 5\*(Aq to 3\*(Aq\&. It is nonsensical to provide a larger value for this parameter than for the Maximum (local) Complementarity parameter because the score of a local alignment will always be at least as great as the score of a global alignment\&. Default value: 3\&.00
+.RE
+.SS "Primer penalty weights"
+.PP
+\fB\-maxendstability\fR \fIfloat\fR
+.RS 4
+The maximum stability for the five 3\*(Aq bases of a forward or reverse primer\&. Bigger numbers mean more stable 3\*(Aq ends\&. The value is the maximum delta G for duplex disruption for the five 3\*(Aq bases as calculated using the nearest neighbor parameters published in Breslauer, Frank, Bloecker and Marky, Proc\&. Natl\&. Acad\&. Sci\&. USA, vol 83, pp 3746\-3750\&. EPrimer3 uses a completely permissive default value for backward compatibility (which we may change in the next release)\&. Rychlik recommends a maximum value of 9 (Wojciech Rychlik, \*(AqSelection of Primers for Polymerase Chain Reaction\*(Aq in BA White, Ed\&., \*(AqMethods in Molecular Biology, Vol\&. 15: PCR Protocols: Current Methods and Applications\*(Aq, 1993, pp 31\-40, Humana Press, Totowa NJ)\&. Default value: 9\&.0
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+eprimer3 is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/codcmp.1e
+++ emboss-6.4.0/debian/manpages/codcmp.1e
@@ -0,0 +1,76 @@
+'\" t
+.\"     Title: CODCMP
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "CODCMP" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+codcmp \- Codon usage table comparison
+.SH "SYNOPSIS"
+.HP \w'\fBcodcmp\fR\ 'u
+\fBcodcmp\fR \fB\-first\ \fR\fB\fIcodon\fR\fR \fB\-second\ \fR\fB\fIcodon\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBcodcmp\fR\ 'u
+\fBcodcmp\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBcodcmp\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Codon usage" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-first\fR \fIcodon\fR
+.RS 4
+First codon usage file
+.RE
+.PP
+\fB\-second\fR \fIcodon\fR
+.RS 4
+Second codon usage file for comparison
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+codcmp is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/transeq.1e
+++ emboss-6.4.0/debian/manpages/transeq.1e
@@ -0,0 +1,101 @@
+'\" t
+.\"     Title: TRANSEQ
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "TRANSEQ" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+transeq \- Translate nucleic acid sequences
+.SH "SYNOPSIS"
+.HP \w'\fBtranseq\fR\ 'u
+\fBtranseq\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR [\fB\-frame\ \fR\fB\fIlist\fR\fR] [\fB\-table\ \fR\fB\fIlist\fR\fR] [\fB\-regions\ \fR\fB\fIrange\fR\fR] [\fB\-trim\ \fR\fB\fIboolean\fR\fR] [\fB\-clean\ \fR\fB\fIboolean\fR\fR] \fB\-alternative\ \fR\fB\fIboolean\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR
+.HP \w'\fBtranseq\fR\ 'u
+\fBtranseq\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBtranseq\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Translation" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqall\fR
+.RS 4
+.RE
+.SS "Additional section"
+.PP
+\fB\-frame\fR \fIlist\fR
+.RS 4
+Default value: 1
+.RE
+.PP
+\fB\-table\fR \fIlist\fR
+.RS 4
+.RE
+.PP
+\fB\-regions\fR \fIrange\fR
+.RS 4
+Regions to translate\&. If this is left blank, then the complete sequence is translated\&. A set of regions is specified by a set of pairs of positions\&. The positions are integers\&. They are separated by any non\-digit, non\-alpha character\&. Examples of region specifications are: 24\-45, 56\-78 1:45, 67=99;765\&.\&.888 1,5,8,10,23,45,57,99 Note: you should not try to use this option with any other frame than the default, \-frame=1
+.RE
+.PP
+\fB\-trim\fR \fIboolean\fR
+.RS 4
+This removes all \*(AqX\*(Aq and \*(Aq*\*(Aq characters from the right end of the translation\&. The trimming process starts at the end and continues until the next character is not a \*(AqX\*(Aq or a \*(Aq*\*(Aq Default value: N
+.RE
+.PP
+\fB\-clean\fR \fIboolean\fR
+.RS 4
+This changes all STOP codon positions from the \*(Aq*\*(Aq character to \*(AqX\*(Aq (an unknown residue)\&. This is useful because some programs will not accept protein sequences with \*(Aq*\*(Aq characters in them\&. Default value: N
+.RE
+.SS "Advanced section"
+.PP
+\fB\-alternative\fR \fIboolean\fR
+.RS 4
+The default definition of frame \*(Aq\-1\*(Aq is the reverse\-complement of the set of codons used in frame 1\&. (Frame \-2 is the set of codons used by frame 2, similarly frames \-3 and 3)\&. This is a common standard, used by the Staden package and other programs\&. If you prefer to define frame \*(Aq\-1\*(Aq as using the set of codons starting with the last codon of the sequence, then set this to be true\&. Default value: N
+.RE
+.SS "Output section"
+.PP
+\fB\-outseq\fR \fIseqoutall\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+transeq is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/drfindformat.1e
+++ emboss-6.4.0/debian/manpages/drfindformat.1e
@@ -0,0 +1,82 @@
+'\" t
+.\"     Title: DRFINDFORMAT
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "DRFINDFORMAT" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+drfindformat \- Find public databases by format
+.SH "SYNOPSIS"
+.HP \w'\fBdrfindformat\fR\ 'u
+\fBdrfindformat\fR \fB\-query\ \fR\fB\fIstring\fR\fR \fB\-sensitive\ \fR\fB\fIboolean\fR\fR \fB\-subclasses\ \fR\fB\fIboolean\fR\fR \fB\-drfindformat\ \fR\fB\fIoutresource\fR\fR
+.HP \w'\fBdrfindformat\fR\ 'u
+\fBdrfindformat\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBdrfindformat\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Ontology:EDAM,Data retrieval:Resource data" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-query\fR \fIstring\fR
+.RS 4
+.RE
+.SS "Additional section"
+.SS "Advanced section"
+.PP
+\fB\-sensitive\fR \fIboolean\fR
+.RS 4
+By default, the query keywords are matched against the EDAM term names (and synonyms) only\&. This option also matches the keywords against the EDAM term definitions and will therefore (typically) report more matches\&. Default value: N
+.RE
+.PP
+\fB\-subclasses\fR \fIboolean\fR
+.RS 4
+Extend the query matches to include all terms which are specialisations (EDAM sub\-classes) of the matched type\&. Default value: Y
+.RE
+.SS "Output section"
+.PP
+\fB\-drfindformat\fR \fIoutresource\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+drfindformat is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/dbigcg.1e
+++ emboss-6.4.0/debian/manpages/dbigcg.1e
@@ -0,0 +1,130 @@
+'\" t
+.\"     Title: DBIGCG
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "DBIGCG" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+dbigcg \- Index a GCG formatted database
+.SH "SYNOPSIS"
+.HP \w'\fBdbigcg\fR\ 'u
+\fBdbigcg\fR \fB\-dbname\ \fR\fB\fIstring\fR\fR \fB\-idformat\ \fR\fB\fIlist\fR\fR \fB\-directory\ \fR\fB\fIdirectory\fR\fR \fB\-filenames\ \fR\fB\fIstring\fR\fR \fB\-release\ \fR\fB\fIstring\fR\fR \fB\-date\ \fR\fB\fIstring\fR\fR \fB\-fields\ \fR\fB\fIlist\fR\fR \fB\-exclude\ \fR\fB\fIstring\fR\fR \fB\-maxindex\ \fR\fB\fIinteger\fR\fR \fB\-sortoptions\ \fR\fB\fIstring\fR\fR \fB\-systemsort\ \fR\fB\fIboolean\fR\fR \fB\-cleanup\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR \fB\-indexoutdir\ \fR\fB\fIoutdir\fR\fR
+.HP \w'\fBdbigcg\fR\ 'u
+\fBdbigcg\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBdbigcg\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Database indexing" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-dbname\fR \fIstring\fR
+.RS 4
+.RE
+.PP
+\fB\-idformat\fR \fIlist\fR
+.RS 4
+Default value: EMBL
+.RE
+.PP
+\fB\-directory\fR \fIdirectory\fR
+.RS 4
+Default value: \&.
+.RE
+.PP
+\fB\-filenames\fR \fIstring\fR
+.RS 4
+Default value: *\&.seq
+.RE
+.SS "Required section"
+.PP
+\fB\-release\fR \fIstring\fR
+.RS 4
+Default value: 0\&.0
+.RE
+.PP
+\fB\-date\fR \fIstring\fR
+.RS 4
+Default value: 00/00/00
+.RE
+.SS "Advanced section"
+.PP
+\fB\-fields\fR \fIlist\fR
+.RS 4
+Default value: acc
+.RE
+.PP
+\fB\-exclude\fR \fIstring\fR
+.RS 4
+.RE
+.PP
+\fB\-maxindex\fR \fIinteger\fR
+.RS 4
+.RE
+.PP
+\fB\-sortoptions\fR \fIstring\fR
+.RS 4
+Sort options, typically \*(Aq\-T \&.\*(Aq to use current directory for work files and \*(Aq\-k 1,1\*(Aq to force GNU sort to use the first field Default value: \-T \&. \-k 1,1
+.RE
+.PP
+\fB\-systemsort\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-cleanup\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.PP
+\fB\-indexoutdir\fR \fIoutdir\fR
+.RS 4
+Default value: \&.
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+dbigcg is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/seqxrefall.1e
+++ emboss-6.4.0/debian/manpages/seqxrefall.1e
@@ -0,0 +1,85 @@
+'\" t
+.\"     Title: SEQXREFALL
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "SEQXREFALL" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+seqxrefall \- Retrieve all cross\-references for a sequence record
+.SH "SYNOPSIS"
+.HP \w'\fBseqxrefall\fR\ 'u
+\fBseqxrefall\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR \fB\-dbref\ \fR\fB\fIdatafile\fR\fR \fB\-format\ \fR\fB\fIselection\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBseqxrefall\fR\ 'u
+\fBseqxrefall\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBseqxrefall\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Information" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIsequence\fR
+.RS 4
+The sequence for which cross\-references will be retrieved\&.
+.RE
+.PP
+\fB\-dbref\fR \fIdatafile\fR
+.RS 4
+File of database information including identifier, description, type, URL etc\&. Default value: dbref\&.dat
+.RE
+.SS "Required section"
+.PP
+\fB\-format\fR \fIselection\fR
+.RS 4
+This specifies the format of the output file Default value: 1
+.RE
+.SS "Additional section"
+.SS "Advanced section"
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+Output file containing list of cross\-references
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+seqxrefall is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/seqmatchall.1e
+++ emboss-6.4.0/debian/manpages/seqmatchall.1e
@@ -0,0 +1,76 @@
+'\" t
+.\"     Title: SEQMATCHALL
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "SEQMATCHALL" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+seqmatchall \- All\-against\-all word comparison of a sequence set
+.SH "SYNOPSIS"
+.HP \w'\fBseqmatchall\fR\ 'u
+\fBseqmatchall\fR \fB\-sequence\ \fR\fB\fIseqset\fR\fR \fB\-wordsize\ \fR\fB\fIinteger\fR\fR \fB\-outfile\ \fR\fB\fIalign\fR\fR
+.HP \w'\fBseqmatchall\fR\ 'u
+\fBseqmatchall\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBseqmatchall\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Alignment:Local" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqset\fR
+.RS 4
+.RE
+.SS "Required section"
+.PP
+\fB\-wordsize\fR \fIinteger\fR
+.RS 4
+Default value: 4
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIalign\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+seqmatchall is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/dbxobo.1e
+++ emboss-6.4.0/debian/manpages/dbxobo.1e
@@ -0,0 +1,121 @@
+'\" t
+.\"     Title: DBXOBO
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "DBXOBO" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+dbxobo \- Index an obo ontology using b+tree indices
+.SH "SYNOPSIS"
+.HP \w'\fBdbxobo\fR\ 'u
+\fBdbxobo\fR \fB\-dbname\ \fR\fB\fIstring\fR\fR \fB\-standardname\ \fR\fB\fIstring\fR\fR \fB\-dbresource\ \fR\fB\fIstring\fR\fR \fB\-directory\ \fR\fB\fIdirectory\fR\fR \fB\-filenames\ \fR\fB\fIstring\fR\fR \fB\-fields\ \fR\fB\fIlist\fR\fR \fB\-compressed\ \fR\fB\fIboolean\fR\fR \fB\-release\ \fR\fB\fIstring\fR\fR \fB\-date\ \fR\fB\fIstring\fR\fR \fB\-exclude\ \fR\fB\fIstring\fR\fR \fB\-indexoutdir\ \fR\fB\fIoutdir\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBdbxobo\fR\ 'u
+\fBdbxobo\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBdbxobo\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Database indexing" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-dbname\fR \fIstring\fR
+.RS 4
+.RE
+.PP
+\fB\-standardname\fR \fIstring\fR
+.RS 4
+Default value: $(dbname)
+.RE
+.PP
+\fB\-dbresource\fR \fIstring\fR
+.RS 4
+Default value: oboresource
+.RE
+.PP
+\fB\-directory\fR \fIdirectory\fR
+.RS 4
+Default value: \&.
+.RE
+.PP
+\fB\-filenames\fR \fIstring\fR
+.RS 4
+Default value: *\&.obo
+.RE
+.SS "Required section"
+.PP
+\fB\-fields\fR \fIlist\fR
+.RS 4
+Default value: *
+.RE
+.PP
+\fB\-compressed\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.SS "Advanced section"
+.PP
+\fB\-release\fR \fIstring\fR
+.RS 4
+Default value: 0\&.0
+.RE
+.PP
+\fB\-date\fR \fIstring\fR
+.RS 4
+Default value: 00/00/00
+.RE
+.PP
+\fB\-exclude\fR \fIstring\fR
+.RS 4
+.RE
+.SS "Output section"
+.PP
+\fB\-indexoutdir\fR \fIoutdir\fR
+.RS 4
+Default value: \&.
+.RE
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+dbxobo is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/nthseqset.1e
+++ emboss-6.4.0/debian/manpages/nthseqset.1e
@@ -0,0 +1,80 @@
+'\" t
+.\"     Title: NTHSEQSET
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "NTHSEQSET" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+nthseqset \- Reads and writes (returns) one set of sequences from many
+.SH "SYNOPSIS"
+.HP \w'\fBnthseqset\fR\ 'u
+\fBnthseqset\fR \fB\-feature\ \fR\fB\fIboolean\fR\fR \fB\-sequence\ \fR\fB\fIseqsetall\fR\fR \fB\-number\ \fR\fB\fIinteger\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR
+.HP \w'\fBnthseqset\fR\ 'u
+\fBnthseqset\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBnthseqset\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-feature\fR \fIboolean\fR
+.RS 4
+.RE
+.PP
+\fB\-sequence\fR \fIseqsetall\fR
+.RS 4
+.RE
+.SS "Required section"
+.PP
+\fB\-number\fR \fIinteger\fR
+.RS 4
+Default value: 1
+.RE
+.SS "Output section"
+.PP
+\fB\-outseq\fR \fIseqoutall\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+nthseqset is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/ajbad.1e
+++ emboss-6.4.0/debian/manpages/ajbad.1e
@@ -0,0 +1,108 @@
+'\" t
+.\"     Title: AJBAD
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "AJBAD" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+ajbad \- Test file for ACD parsing
+.SH "SYNOPSIS"
+.HP \w'\fBajbad\fR\ 'u
+\fBajbad\fR \fB\-typea\ \fR\fB\fIstring\fR\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR \fB\-bsequence\ \fR\fB\fIsequence\fR\fR \fB\-eco\ \fR\fB\fIcodon\fR\fR \fB\-typeb\ \fR\fB\fIstring\fR\fR \fB\-date\ \fR\fB\fIstring\fR\fR \fB\-a\ \fR\fB\fIinteger\fR\fR \fB\-b\ \fR\fB\fIinteger\fR\fR \fB\-c\ \fR\fB\fIfloat\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBajbad\fR\ 'u
+\fBajbad\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBajbad\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Test" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-typea\fR \fIstring\fR
+.RS 4
+.RE
+.PP
+\fB\-sequence\fR \fIsequence\fR
+.RS 4
+.RE
+.PP
+\fB\-bsequence\fR \fIsequence\fR
+.RS 4
+.RE
+.PP
+\fB\-eco\fR \fIcodon\fR
+.RS 4
+.RE
+.SS "Required section"
+.PP
+\fB\-typeb\fR \fIstring\fR
+.RS 4
+Default value: $(seqa\&.type)
+.RE
+.PP
+\fB\-date\fR \fIstring\fR
+.RS 4
+Default value: 00/00/00
+.RE
+.SS "Advanced section"
+.PP
+\fB\-a\fR \fIinteger\fR
+.RS 4
+.RE
+.PP
+\fB\-b\fR \fIinteger\fR
+.RS 4
+Default value: 15
+.RE
+.PP
+\fB\-c\fR \fIfloat\fR
+.RS 4
+Default value: 1\&.6
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+ajbad is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/yank.1e
+++ emboss-6.4.0/debian/manpages/yank.1e
@@ -0,0 +1,75 @@
+'\" t
+.\"     Title: YANK
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "YANK" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+yank \- Add a sequence reference (a full USA) to a list file
+.SH "SYNOPSIS"
+.HP \w'\fByank\fR\ 'u
+\fByank\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR \fB\-newfile\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fByank\fR\ 'u
+\fByank\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fByank\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIsequence\fR
+.RS 4
+.RE
+.SS "Output section"
+.PP
+\fB\-newfile\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+yank is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/dbshowquery.1e
+++ emboss-6.4.0/debian/manpages/dbshowquery.1e
@@ -0,0 +1,91 @@
+'\" t
+.\"     Title: DBSHOWQUERY
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "DBSHOWQUERY" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+dbshowquery \- Show possible database queries that use a given data identifier
+.SH "SYNOPSIS"
+.HP \w'\fBdbshowquery\fR\ 'u
+\fBdbshowquery\fR \fB\-identifier\ \fR\fB\fIstring\fR\fR \fB\-database\ \fR\fB\fIstring\fR\fR \fB\-datatype\ \fR\fB\fIstring\fR\fR [\fB\-outfile\ \fR\fB\fIoutfile\fR\fR] [\fB\-html\ \fR\fB\fIboolean\fR\fR]
+.HP \w'\fBdbshowquery\fR\ 'u
+\fBdbshowquery\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBdbshowquery\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Information" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-identifier\fR \fIstring\fR
+.RS 4
+This is a data identifier (e\&.g\&. a sequence accession number) that is used to specify the data (of type \*(Aqdatatype\*(Aq) to retrieve\&. If you\*(Aqre unsure of the data identifier(s) that are used for a given query (database/datatype) use dbtellquery\&. The types of data identifier are listed under the \*(AqData identifier\*(Aq branch of the EDAM ontology (http://edamontology\&.sourceforge\&.net/)\&. For example values, see the catalogue of public databases in the EMBOSS data file DRCAT\&.dat\&. If you have a data identifier but are unsure of its type, use idtell\&.
+.RE
+.SS "Required section"
+.SS "Additional section"
+.SS "Advanced section"
+.PP
+\fB\-database\fR \fIstring\fR
+.RS 4
+This is the name of a database from the catalogue of public databases in the EMBOSS data file DRCAT\&.dat\&. If you are unsure of the available databases use drfind\&. If you have a database name but are not sure its valid, use isdbname\&.
+.RE
+.PP
+\fB\-datatype\fR \fIstring\fR
+.RS 4
+This is the name of a retrievable datatype from the catalogue of public databases in the EMBOSS data file DRCAT\&.dat\&. The names are terms from the \*(Aqdata\*(Aq branch of the EDAM ontology, http://edamontology\&.sourceforge\&.net/\&. If you are unsure of the available retrievable datatypes for a given database, use dbtellquery\&. If you have a datatype name but are not sure its valid, use isdbdata\&.
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+Default value: stdout
+.RE
+.SS "Html section"
+.PP
+\fB\-html\fR \fIboolean\fR
+.RS 4
+If you are sending the output to a file, this will format it for displaying as a table in a WWW document\&. Default value: N
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+dbshowquery is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/maskseq.1e
+++ emboss-6.4.0/debian/manpages/maskseq.1e
@@ -0,0 +1,87 @@
+'\" t
+.\"     Title: MASKSEQ
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "MASKSEQ" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+maskseq \- Write a sequence with masked regions
+.SH "SYNOPSIS"
+.HP \w'\fBmaskseq\fR\ 'u
+\fBmaskseq\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR \fB\-regions\ \fR\fB\fIrange\fR\fR [\fB\-tolower\ \fR\fB\fItoggle\fR\fR] \fB\-maskchar\ \fR\fB\fIstring\fR\fR \fB\-outseq\ \fR\fB\fIseqout\fR\fR
+.HP \w'\fBmaskseq\fR\ 'u
+\fBmaskseq\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBmaskseq\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIsequence\fR
+.RS 4
+.RE
+.SS "Required section"
+.PP
+\fB\-regions\fR \fIrange\fR
+.RS 4
+Regions to mask\&. A set of regions is specified by a set of pairs of positions\&. The positions are integers\&. They are separated by any non\-digit, non\-alpha character\&. Examples of region specifications are: 24\-45, 56\-78 1:45, 67=99;765\&.\&.888 1,5,8,10,23,45,57,99
+.RE
+.SS "Additional section"
+.PP
+\fB\-tolower\fR \fItoggle\fR
+.RS 4
+The region can be \*(Aqmasked\*(Aq by converting the sequence characters to lower\-case, some non\-EMBOSS programs e\&.g\&. fasta can interpret this as a masked region\&. The sequence is unchanged apart from the case change\&. You might like to ensure that the whole sequence is in upper\-case before masking the specified regions to lower\-case by using the \*(Aq\-supper\*(Aq flag\&. Default value: N
+.RE
+.PP
+\fB\-maskchar\fR \fIstring\fR
+.RS 4
+Character to use when masking\&. Default is \*(AqX\*(Aq for protein sequences, \*(AqN\*(Aq for nucleic sequences\&. If the mask character is set to be the SPACE character or a null character, then the sequence is \*(Aqmasked\*(Aq by changing it to lower\-case, just as with the \*(Aq\-lowercase\*(Aq flag\&. Default value: @($(acdprotein)?X:N)
+.RE
+.SS "Output section"
+.PP
+\fB\-outseq\fR \fIseqout\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+maskseq is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/acdlog.1e
+++ emboss-6.4.0/debian/manpages/acdlog.1e
@@ -0,0 +1,60 @@
+'\" t
+.\"     Title: ACDLOG
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "ACDLOG" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+acdlog \- Test application ACD file processing and trace data structures
+.SH "SYNOPSIS"
+.HP \w'\fBacdlog\fR\ 'u
+\fBacdlog\fR
+.HP \w'\fBacdlog\fR\ 'u
+\fBacdlog\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBacdlog\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Acd,Data retrieval:Tool data" command group(s)\&.
+.SH "OPTIONS"
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+acdlog is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/redata.1e
+++ emboss-6.4.0/debian/manpages/redata.1e
@@ -0,0 +1,86 @@
+'\" t
+.\"     Title: REDATA
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "REDATA" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+redata \- Retrieve information from REBASE restriction enzyme database
+.SH "SYNOPSIS"
+.HP \w'\fBredata\fR\ 'u
+\fBredata\fR \fB\-enzyme\ \fR\fB\fIstring\fR\fR \fB\-isoschizomers\ \fR\fB\fIboolean\fR\fR \fB\-references\ \fR\fB\fIboolean\fR\fR \fB\-suppliers\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBredata\fR\ 'u
+\fBredata\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBredata\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Restriction" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-enzyme\fR \fIstring\fR
+.RS 4
+Enter the name of the restriction enzyme that you wish to get details of\&. The names often have a \*(AqI\*(Aq in them \- this is a capital \*(Aqi\*(Aq, not a \*(Aq1\*(Aq or an \*(Aql\*(Aq\&. The names are case\-independent (\*(AqAaeI\*(Aq is the same as \*(Aqaaei\*(Aq) Default value: BamHI
+.RE
+.SS "Output section"
+.PP
+\fB\-isoschizomers\fR \fIboolean\fR
+.RS 4
+Show other enzymes with this specificity\&. (Isoschizomers) Default value: Y
+.RE
+.PP
+\fB\-references\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-suppliers\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+redata is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/martattributes.1e
+++ emboss-6.4.0/debian/manpages/martattributes.1e
@@ -0,0 +1,87 @@
+'\" t
+.\"     Title: MARTATTRIBUTES
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "MARTATTRIBUTES" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+martattributes \- Return attributes from a mart dataset from a mart host
+.SH "SYNOPSIS"
+.HP \w'\fBmartattributes\fR\ 'u
+\fBmartattributes\fR \fB\-dataset\ \fR\fB\fIstring\fR\fR \fB\-host\ \fR\fB\fIstring\fR\fR \fB\-path\ \fR\fB\fIstring\fR\fR \fB\-port\ \fR\fB\fIinteger\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBmartattributes\fR\ 'u
+\fBmartattributes\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBmartattributes\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-dataset\fR \fIstring\fR
+.RS 4
+Default value: oanatinus_gene_ensembl
+.RE
+.SS "Advanced section"
+.PP
+\fB\-host\fR \fIstring\fR
+.RS 4
+Default value: www\&.biomart\&.org
+.RE
+.PP
+\fB\-path\fR \fIstring\fR
+.RS 4
+Default value: /biomart/martservice
+.RE
+.PP
+\fB\-port\fR \fIinteger\fR
+.RS 4
+Default value: 80
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+martattributes is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/newcoils.1e
+++ emboss-6.4.0/debian/manpages/newcoils.1e
@@ -0,0 +1,103 @@
+'\" t
+.\"     Title: NEWCOILS
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "NEWCOILS" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+newcoils \- Predicts coils protein secondary structure
+.SH "SYNOPSIS"
+.HP \w'\fBnewcoils\fR\ 'u
+\fBnewcoils\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-datafile\ \fR\fB\fIdatafile\fR\fR \fB\-window\ \fR\fB\fIinteger\fR\fR \fB\-weighted\ \fR\fB\fIinteger\fR\fR \fB\-verb\ \fR\fB\fIinteger\fR\fR \fB\-mode\ \fR\fB\fIinteger\fR\fR \fB\-minseg\ \fR\fB\fIinteger\fR\fR \fB\-minp\ \fR\fB\fIfloat\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBnewcoils\fR\ 'u
+\fBnewcoils\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBnewcoils\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Protein:2D Structure" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqall\fR
+.RS 4
+.RE
+.PP
+\fB\-datafile\fR \fIdatafile\fR
+.RS 4
+Default value: Enewcoils\&.mat
+.RE
+.SS "Required section"
+.PP
+\fB\-window\fR \fIinteger\fR
+.RS 4
+Default value: 21
+.RE
+.PP
+\fB\-weighted\fR \fIinteger\fR
+.RS 4
+.RE
+.PP
+\fB\-verb\fR \fIinteger\fR
+.RS 4
+.RE
+.PP
+\fB\-mode\fR \fIinteger\fR
+.RS 4
+.RE
+.PP
+\fB\-minseg\fR \fIinteger\fR
+.RS 4
+Default value: 1
+.RE
+.PP
+\fB\-minp\fR \fIfloat\fR
+.RS 4
+Default value: 0\&.50
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+newcoils is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/origunion.1e
+++ emboss-6.4.0/debian/manpages/origunion.1e
@@ -0,0 +1,70 @@
+'\" t
+.\"     Title: ORIGUNION
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "ORIGUNION" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+origunion \- Reads sequence fragments and builds one sequence
+.SH "SYNOPSIS"
+.HP \w'\fBorigunion\fR\ 'u
+\fBorigunion\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-outseq\ \fR\fB\fIseqout\fR\fR
+.HP \w'\fBorigunion\fR\ 'u
+\fBorigunion\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBorigunion\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqall\fR
+.RS 4
+.RE
+.SS "Output section"
+.PP
+\fB\-outseq\fR \fIseqout\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+origunion is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/dreg.1e
+++ emboss-6.4.0/debian/manpages/dreg.1e
@@ -0,0 +1,74 @@
+'\" t
+.\"     Title: DREG
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "DREG" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+dreg \- Regular expression search of nucleotide sequence(s)
+.SH "SYNOPSIS"
+.HP \w'\fBdreg\fR\ 'u
+\fBdreg\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-pattern\ \fR\fB\fIregexp\fR\fR \fB\-outfile\ \fR\fB\fIreport\fR\fR
+.HP \w'\fBdreg\fR\ 'u
+\fBdreg\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBdreg\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Motifs" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqall\fR
+.RS 4
+.RE
+.PP
+\fB\-pattern\fR \fIregexp\fR
+.RS 4
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIreport\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+dreg is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/ontoisobsolete.1e
+++ emboss-6.4.0/debian/manpages/ontoisobsolete.1e
@@ -0,0 +1,73 @@
+'\" t
+.\"     Title: ONTOISOBSOLETE
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "ONTOISOBSOLETE" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+ontoisobsolete \- Report whether an ontology term id is obsolete
+.SH "SYNOPSIS"
+.HP \w'\fBontoisobsolete\fR\ 'u
+\fBontoisobsolete\fR \fB\-oboterms\ \fR\fB\fIobo\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBontoisobsolete\fR\ 'u
+\fBontoisobsolete\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBontoisobsolete\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Ontology,Data retrieval:Ontology data" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-oboterms\fR \fIobo\fR
+.RS 4
+.RE
+.SS "Additional section"
+.SS "Advanced section"
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+Default value: stdout
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+ontoisobsolete is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/showserver.1e
+++ emboss-6.4.0/debian/manpages/showserver.1e
@@ -0,0 +1,168 @@
+'\" t
+.\"     Title: SHOWSERVER
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "SHOWSERVER" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+showserver \- Displays information on configured servers
+.SH "SYNOPSIS"
+.HP \w'\fBshowserver\fR\ 'u
+\fBshowserver\fR [\fB\-server\ \fR\fB\fIstring\fR\fR] [\fB\-showtypes\ \fR\fB\fIlist\fR\fR] [\fB\-html\ \fR\fB\fIboolean\fR\fR] [\fB\-full\ \fR\fB\fIboolean\fR\fR] [\fB\-methods\ \fR\fB\fIboolean\fR\fR] [\fB\-count\ \fR\fB\fIboolean\fR\fR] [\fB\-cachefile\ \fR\fB\fIboolean\fR\fR] [\fB\-url\ \fR\fB\fIboolean\fR\fR] [\fB\-fields\ \fR\fB\fIboolean\fR\fR] [\fB\-defined\ \fR\fB\fIboolean\fR\fR] [\fB\-serverversion\ \fR\fB\fIboolean\fR\fR] [\fB\-sortby\ \fR\fB\fIlist\fR\fR] \fB\-only\ \fR\fB\fItoggle\fR\fR \fB\-heading\ \fR\fB\fIboolean\fR\fR \fB\-scope\ \fR\fB\fIboolean\fR\fR \fB\-type\ \fR\fB\fIboolean\fR\fR \fB\-id\ \fR\fB\fIboolean\fR\fR \fB\-query\ \fR\fB\fIboolean\fR\fR \fB\-all\ \fR\fB\fIboolean\fR\fR \fB\-comment\ \fR\fB\fIboolean\fR\fR [\fB\-outfile\ \fR\fB\fIoutfile\fR\fR]
+.HP \w'\fBshowserver\fR\ 'u
+\fBshowserver\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBshowserver\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Data resources" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-server\fR \fIstring\fR
+.RS 4
+.RE
+.SS "Additional section"
+.PP
+\fB\-showtypes\fR \fIlist\fR
+.RS 4
+Default value: *
+.RE
+.PP
+\fB\-html\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-full\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-methods\fR \fIboolean\fR
+.RS 4
+This displays the access methods that can be used on this server, for all, query or ID access Default value: $(full)
+.RE
+.PP
+\fB\-count\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-cachefile\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-url\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-fields\fR \fIboolean\fR
+.RS 4
+This displays the search fields that can be used on this server, other than the standard \*(Aqid\*(Aq or \*(Aqacc\*(Aq fields\&. Default value: $(full)
+.RE
+.PP
+\fB\-defined\fR \fIboolean\fR
+.RS 4
+This displays a short name for the file containing the server definition Default value: $(full)
+.RE
+.PP
+\fB\-serverversion\fR \fIboolean\fR
+.RS 4
+Default value: $(full)
+.RE
+.PP
+\fB\-sortby\fR \fIlist\fR
+.RS 4
+Default value: type
+.RE
+.SS "Advanced section"
+.PP
+\fB\-only\fR \fItoggle\fR
+.RS 4
+This is a way of shortening the command line if you only want a few standard columns to be displayed\&. Instead of specifying: \*(Aq\-nohead \-notype \-noid \-noquery \-noall\*(Aq to get only the comment output, you can specify \*(Aq\-only \-comment\*(Aq Default value: N
+.RE
+.PP
+\fB\-heading\fR \fIboolean\fR
+.RS 4
+Default value: @(!$(only))
+.RE
+.PP
+\fB\-scope\fR \fIboolean\fR
+.RS 4
+Default value: @(!$(only))
+.RE
+.PP
+\fB\-type\fR \fIboolean\fR
+.RS 4
+Default value: @(!$(only))
+.RE
+.PP
+\fB\-id\fR \fIboolean\fR
+.RS 4
+Default value: @(!$(only))
+.RE
+.PP
+\fB\-query\fR \fIboolean\fR
+.RS 4
+Default value: @(!$(only))
+.RE
+.PP
+\fB\-all\fR \fIboolean\fR
+.RS 4
+Default value: @(!$(only))
+.RE
+.PP
+\fB\-comment\fR \fIboolean\fR
+.RS 4
+Default value: @(!$(only))
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+Default value: stdout
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+showserver is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/ajfeatest.1e
+++ emboss-6.4.0/debian/manpages/ajfeatest.1e
@@ -0,0 +1,70 @@
+'\" t
+.\"     Title: AJFEATEST
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "AJFEATEST" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+ajfeatest \- Reads and writes (returns) a sequence and its features
+.SH "SYNOPSIS"
+.HP \w'\fBajfeatest\fR\ 'u
+\fBajfeatest\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR \fB\-outseq\ \fR\fB\fIseqout\fR\fR
+.HP \w'\fBajfeatest\fR\ 'u
+\fBajfeatest\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBajfeatest\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Test" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIsequence\fR
+.RS 4
+.RE
+.SS "Output section"
+.PP
+\fB\-outseq\fR \fIseqout\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+ajfeatest is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/est2genome.1e
+++ emboss-6.4.0/debian/manpages/est2genome.1e
@@ -0,0 +1,150 @@
+'\" t
+.\"     Title: EST2GENOME
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "EST2GENOME" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+est2genome \- Align EST sequences to genomic DNA sequence
+.SH "SYNOPSIS"
+.HP \w'\fBest2genome\fR\ 'u
+\fBest2genome\fR \fB\-estsequence\ \fR\fB\fIseqall\fR\fR \fB\-genomesequence\ \fR\fB\fIsequence\fR\fR [\fB\-match\ \fR\fB\fIinteger\fR\fR] [\fB\-mismatch\ \fR\fB\fIinteger\fR\fR] [\fB\-gappenalty\ \fR\fB\fIinteger\fR\fR] [\fB\-intronpenalty\ \fR\fB\fIinteger\fR\fR] [\fB\-splicepenalty\ \fR\fB\fIinteger\fR\fR] [\fB\-minscore\ \fR\fB\fIinteger\fR\fR] \fB\-reverse\ \fR\fB\fIboolean\fR\fR \fB\-usesplice\ \fR\fB\fIboolean\fR\fR \fB\-mode\ \fR\fB\fIlist\fR\fR \fB\-best\ \fR\fB\fIboolean\fR\fR \fB\-space\ \fR\fB\fIfloat\fR\fR \fB\-shuffle\ \fR\fB\fIinteger\fR\fR \fB\-seed\ \fR\fB\fIinteger\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR \fB\-align\ \fR\fB\fIboolean\fR\fR \fB\-width\ \fR\fB\fIinteger\fR\fR
+.HP \w'\fBest2genome\fR\ 'u
+\fBest2genome\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBest2genome\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Alignment:Global" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-estsequence\fR \fIseqall\fR
+.RS 4
+.RE
+.PP
+\fB\-genomesequence\fR \fIsequence\fR
+.RS 4
+.RE
+.SS "Additional section"
+.PP
+\fB\-match\fR \fIinteger\fR
+.RS 4
+Default value: 1
+.RE
+.PP
+\fB\-mismatch\fR \fIinteger\fR
+.RS 4
+Default value: 1
+.RE
+.PP
+\fB\-gappenalty\fR \fIinteger\fR
+.RS 4
+Cost for deleting a single base in either sequence, excluding introns Default value: 2
+.RE
+.PP
+\fB\-intronpenalty\fR \fIinteger\fR
+.RS 4
+Cost for an intron, independent of length\&. Default value: 40
+.RE
+.PP
+\fB\-splicepenalty\fR \fIinteger\fR
+.RS 4
+Cost for an intron, independent of length and starting/ending on donor\-acceptor sites Default value: 20
+.RE
+.PP
+\fB\-minscore\fR \fIinteger\fR
+.RS 4
+Exclude alignments with scores below this threshold score\&. Default value: 30
+.RE
+.SS "Advanced section"
+.PP
+\fB\-reverse\fR \fIboolean\fR
+.RS 4
+Reverse the orientation of the EST sequence
+.RE
+.PP
+\fB\-usesplice\fR \fIboolean\fR
+.RS 4
+Use donor and acceptor splice sites\&. If you want to ignore donor\-acceptor sites then set this to be false\&. Default value: Y
+.RE
+.PP
+\fB\-mode\fR \fIlist\fR
+.RS 4
+This determines the comparison mode\&. The default value is \*(Aqboth\*(Aq, in which case both strands of the est are compared assuming a forward gene direction (ie GT/AG splice sites), and the best comparison redone assuming a reversed (CT/AC) gene splicing direction\&. The other allowed modes are \*(Aqforward\*(Aq, when just the forward strand is searched, and \*(Aqreverse\*(Aq, ditto for the reverse strand\&. Default value: both
+.RE
+.PP
+\fB\-best\fR \fIboolean\fR
+.RS 4
+You can print out all comparisons instead of just the best one by setting this to be false\&. Default value: Y
+.RE
+.PP
+\fB\-space\fR \fIfloat\fR
+.RS 4
+For linear\-space recursion\&. If product of sequence lengths divided by 4 exceeds this then a divide\-and\-conquer strategy is used to control the memory requirements\&. In this way very long sequences can be aligned\&. If you have a machine with plenty of memory you can raise this parameter (but do not exceed the machine\*(Aqs physical RAM) Default value: 10\&.0
+.RE
+.PP
+\fB\-shuffle\fR \fIinteger\fR
+.RS 4
+.RE
+.PP
+\fB\-seed\fR \fIinteger\fR
+.RS 4
+Default value: 20825
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.PP
+\fB\-align\fR \fIboolean\fR
+.RS 4
+Show the alignment\&. The alignment includes the first and last 5 bases of each intron, together with the intron width\&. The direction of splicing is indicated by angle brackets (forward or reverse) or ???? (unknown)\&.
+.RE
+.PP
+\fB\-width\fR \fIinteger\fR
+.RS 4
+Default value: 50
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+est2genome is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/infoalign.1e
+++ emboss-6.4.0/debian/manpages/infoalign.1e
@@ -0,0 +1,168 @@
+'\" t
+.\"     Title: INFOALIGN
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "INFOALIGN" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+infoalign \- Display basic information about a multiple sequence alignment
+.SH "SYNOPSIS"
+.HP \w'\fBinfoalign\fR\ 'u
+\fBinfoalign\fR \fB\-sequence\ \fR\fB\fIseqset\fR\fR [\fB\-matrix\ \fR\fB\fImatrix\fR\fR] [\fB\-refseq\ \fR\fB\fIstring\fR\fR] \fB\-plurality\ \fR\fB\fIfloat\fR\fR \fB\-identity\ \fR\fB\fIfloat\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-html\ \fR\fB\fIboolean\fR\fR] \fB\-only\ \fR\fB\fIboolean\fR\fR \fB\-heading\ \fR\fB\fIboolean\fR\fR \fB\-usa\ \fR\fB\fIboolean\fR\fR \fB\-name\ \fR\fB\fIboolean\fR\fR \fB\-seqlength\ \fR\fB\fIboolean\fR\fR \fB\-alignlength\ \fR\fB\fIboolean\fR\fR \fB\-gaps\ \fR\fB\fIboolean\fR\fR \fB\-gapcount\ \fR\fB\fIboolean\fR\fR \fB\-idcount\ \fR\fB\fIboolean\fR\fR \fB\-simcount\ \fR\fB\fIboolean\fR\fR \fB\-diffcount\ \fR\fB\fIboolean\fR\fR \fB\-change\ \fR\fB\fIboolean\fR\fR \fB\-weight\ \fR\fB\fIboolean\fR\fR \fB\-description\ \fR\fB\fIboolean\fR\fR
+.HP \w'\fBinfoalign\fR\ 'u
+\fBinfoalign\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBinfoalign\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Alignment:Multiple,Data retrieval:Sequence data" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqset\fR
+.RS 4
+The sequence alignment to be displayed\&.
+.RE
+.PP
+\fB\-matrix\fR \fImatrix\fR
+.RS 4
+This is the scoring matrix file used when comparing sequences\&. By default it is the file \*(AqEBLOSUM62\*(Aq (for proteins) or the file \*(AqEDNAFULL\*(Aq (for nucleic sequences)\&. These files are found in the \*(Aqdata\*(Aq directory of the EMBOSS installation\&.
+.RE
+.PP
+\fB\-refseq\fR \fIstring\fR
+.RS 4
+If you give the number in the alignment or the name of a sequence, it will be taken to be the reference sequence\&. The reference sequence is the one against which all the other sequences are compared\&. If this is set to 0 then the consensus sequence will be used as the reference sequence\&. By default the consensus sequence is used as the reference sequence\&.
+.RE
+.SS "Advanced section"
+.PP
+\fB\-plurality\fR \fIfloat\fR
+.RS 4
+Set a cut\-off for the % of positive scoring matches below which there is no consensus\&. The default plurality is taken as 50% of the total weight of all the sequences in the alignment\&. Default value: 50\&.0
+.RE
+.PP
+\fB\-identity\fR \fIfloat\fR
+.RS 4
+Provides the facility of setting the required number of identities at a position for it to give a consensus\&. Therefore, if this is set to 100% only columns of identities contribute to the consensus\&. Default value: 0\&.0
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+If you enter the name of a file here then this program will write the sequence details into that file\&.
+.RE
+.PP
+\fB\-html\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-only\fR \fIboolean\fR
+.RS 4
+This is a way of shortening the command line if you only want a few things to be displayed\&. Instead of specifying: \*(Aq\-nohead \-nousa \-noname \-noalign \-nogaps \-nogapcount \-nosimcount \-noidcount \-nodiffcount \-noweight\*(Aq to get only the sequence length output, you can specify \*(Aq\-only \-seqlength\*(Aq Default value: N
+.RE
+.PP
+\fB\-heading\fR \fIboolean\fR
+.RS 4
+Default value: @(!$(only))
+.RE
+.PP
+\fB\-usa\fR \fIboolean\fR
+.RS 4
+Default value: @(!$(only))
+.RE
+.PP
+\fB\-name\fR \fIboolean\fR
+.RS 4
+Default value: @(!$(only))
+.RE
+.PP
+\fB\-seqlength\fR \fIboolean\fR
+.RS 4
+Default value: @(!$(only))
+.RE
+.PP
+\fB\-alignlength\fR \fIboolean\fR
+.RS 4
+Default value: @(!$(only))
+.RE
+.PP
+\fB\-gaps\fR \fIboolean\fR
+.RS 4
+Default value: @(!$(only))
+.RE
+.PP
+\fB\-gapcount\fR \fIboolean\fR
+.RS 4
+Default value: @(!$(only))
+.RE
+.PP
+\fB\-idcount\fR \fIboolean\fR
+.RS 4
+Default value: @(!$(only))
+.RE
+.PP
+\fB\-simcount\fR \fIboolean\fR
+.RS 4
+Default value: @(!$(only))
+.RE
+.PP
+\fB\-diffcount\fR \fIboolean\fR
+.RS 4
+Default value: @(!$(only))
+.RE
+.PP
+\fB\-change\fR \fIboolean\fR
+.RS 4
+Default value: @(!$(only))
+.RE
+.PP
+\fB\-weight\fR \fIboolean\fR
+.RS 4
+Default value: @(!$(only))
+.RE
+.PP
+\fB\-description\fR \fIboolean\fR
+.RS 4
+Default value: @(!$(only))
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+infoalign is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/ontoget.1e
+++ emboss-6.4.0/debian/manpages/ontoget.1e
@@ -0,0 +1,82 @@
+'\" t
+.\"     Title: ONTOGET
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "ONTOGET" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+ontoget \- Get ontology term(s)
+.SH "SYNOPSIS"
+.HP \w'\fBontoget\fR\ 'u
+\fBontoget\fR \fB\-oboterms\ \fR\fB\fIobo\fR\fR [\fB\-subclasses\ \fR\fB\fIboolean\fR\fR] [\fB\-obsolete\ \fR\fB\fIboolean\fR\fR] \fB\-outfile\ \fR\fB\fIoutobo\fR\fR
+.HP \w'\fBontoget\fR\ 'u
+\fBontoget\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBontoget\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Ontology,Data retrieval:Ontology data" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-oboterms\fR \fIobo\fR
+.RS 4
+.RE
+.SS "Additional section"
+.PP
+\fB\-subclasses\fR \fIboolean\fR
+.RS 4
+Extend the query matches to include all terms which are specialisations (sub\-classes) of the matched terms\&. Default value: N
+.RE
+.PP
+\fB\-obsolete\fR \fIboolean\fR
+.RS 4
+The default behaviour is to not use or return obsolete terms\&. This option if set will include all terms\&. Default value: N
+.RE
+.SS "Advanced section"
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutobo\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+ontoget is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/msbar.1e
+++ emboss-6.4.0/debian/manpages/msbar.1e
@@ -0,0 +1,111 @@
+'\" t
+.\"     Title: MSBAR
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "MSBAR" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+msbar \- Mutate a sequence
+.SH "SYNOPSIS"
+.HP \w'\fBmsbar\fR\ 'u
+\fBmsbar\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-othersequence\ \fR\fB\fIseqall\fR\fR \fB\-count\ \fR\fB\fIinteger\fR\fR \fB\-point\ \fR\fB\fIlist\fR\fR \fB\-block\ \fR\fB\fIlist\fR\fR \fB\-codon\ \fR\fB\fIlist\fR\fR \fB\-inframe\ \fR\fB\fIboolean\fR\fR \fB\-minimum\ \fR\fB\fIinteger\fR\fR \fB\-maximum\ \fR\fB\fIinteger\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR
+.HP \w'\fBmsbar\fR\ 'u
+\fBmsbar\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBmsbar\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Mutation,Protein:Mutation" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqall\fR
+.RS 4
+.RE
+.PP
+\fB\-othersequence\fR \fIseqall\fR
+.RS 4
+If you require that the resulting mutated sequence should not match a set of other sequences, then you can specify that set of sequences here\&. For example, if you require that the mutated sequence should not be the same as the input sequence, enter the input sequence here\&. If you want the result to be different to previous results of this program, specify the previous result sequences here\&. The program will check that the result does not match the sequences specified here before writing it out\&. If a match is found, then the mutation is started again with a fresh copy of the input sequence\&. If, after 10 such retries, there is still a match to the set of sequence given here, then the matching mutated sequence is written with a warning message\&. Default value: asis:N
+.RE
+.SS "Required section"
+.PP
+\fB\-count\fR \fIinteger\fR
+.RS 4
+Default value: 1
+.RE
+.PP
+\fB\-point\fR \fIlist\fR
+.RS 4
+.RE
+.PP
+\fB\-block\fR \fIlist\fR
+.RS 4
+.RE
+.PP
+\fB\-codon\fR \fIlist\fR
+.RS 4
+Types of codon mutations to perform\&. These are only done if the sequence is nucleic\&.
+.RE
+.SS "Additional section"
+.PP
+\fB\-inframe\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.SS "Advanced section"
+.PP
+\fB\-minimum\fR \fIinteger\fR
+.RS 4
+Default value: 1
+.RE
+.PP
+\fB\-maximum\fR \fIinteger\fR
+.RS 4
+Default value: 10
+.RE
+.SS "Output section"
+.PP
+\fB\-outseq\fR \fIseqoutall\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+msbar is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/wordmatch.1e
+++ emboss-6.4.0/debian/manpages/wordmatch.1e
@@ -0,0 +1,103 @@
+'\" t
+.\"     Title: WORDMATCH
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "WORDMATCH" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+wordmatch \- Finds regions of identity (exact matches) of two sequences
+.SH "SYNOPSIS"
+.HP \w'\fBwordmatch\fR\ 'u
+\fBwordmatch\fR \fB\-asequence\ \fR\fB\fIseqset\fR\fR \fB\-bsequence\ \fR\fB\fIseqall\fR\fR \fB\-wordsize\ \fR\fB\fIinteger\fR\fR [\fB\-dumpalign\ \fR\fB\fItoggle\fR\fR] \fB\-outfile\ \fR\fB\fIalign\fR\fR [\fB\-logfile\ \fR\fB\fIoutfile\fR\fR] [\fB\-dumpfeat\ \fR\fB\fItoggle\fR\fR] \fB\-aoutfeat\ \fR\fB\fIfeatout\fR\fR \fB\-boutfeat\ \fR\fB\fIfeatout\fR\fR
+.HP \w'\fBwordmatch\fR\ 'u
+\fBwordmatch\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBwordmatch\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Alignment:Local" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-asequence\fR \fIseqset\fR
+.RS 4
+.RE
+.PP
+\fB\-bsequence\fR \fIseqall\fR
+.RS 4
+.RE
+.SS "Required section"
+.PP
+\fB\-wordsize\fR \fIinteger\fR
+.RS 4
+Default value: 4
+.RE
+.SS "Output section"
+.PP
+\fB\-dumpalign\fR \fItoggle\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-outfile\fR \fIalign\fR
+.RS 4
+.RE
+.PP
+\fB\-logfile\fR \fIoutfile\fR
+.RS 4
+Statistics on distribution of kmers and matches Default value: wordmatch\&.log
+.RE
+.PP
+\fB\-dumpfeat\fR \fItoggle\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-aoutfeat\fR \fIfeatout\fR
+.RS 4
+.RE
+.PP
+\fB\-boutfeat\fR \fIfeatout\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+wordmatch is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/patmatmotifs.1e
+++ emboss-6.4.0/debian/manpages/patmatmotifs.1e
@@ -0,0 +1,81 @@
+'\" t
+.\"     Title: PATMATMOTIFS
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "PATMATMOTIFS" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+patmatmotifs \- Scan a protein sequence with motifs from the PROSITE database
+.SH "SYNOPSIS"
+.HP \w'\fBpatmatmotifs\fR\ 'u
+\fBpatmatmotifs\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR [\fB\-full\ \fR\fB\fIboolean\fR\fR] [\fB\-prune\ \fR\fB\fIboolean\fR\fR] \fB\-outfile\ \fR\fB\fIreport\fR\fR
+.HP \w'\fBpatmatmotifs\fR\ 'u
+\fBpatmatmotifs\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBpatmatmotifs\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Protein:Motifs" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIsequence\fR
+.RS 4
+.RE
+.SS "Additional section"
+.PP
+\fB\-full\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-prune\fR \fIboolean\fR
+.RS 4
+Ignore simple patterns\&. If this is true then these simple post\-translational modification sites are not reported: myristyl, asn_glycosylation, camp_phospho_site, pkc_phospho_site, ck2_phospho_site, and tyr_phospho_site\&. Default value: Y
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIreport\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+patmatmotifs is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/density.1e
+++ emboss-6.4.0/debian/manpages/density.1e
@@ -0,0 +1,89 @@
+'\" t
+.\"     Title: DENSITY
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "DENSITY" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+density \- Draw a nucleic acid density plot
+.SH "SYNOPSIS"
+.HP \w'\fBdensity\fR\ 'u
+\fBdensity\fR \fB\-seqall\ \fR\fB\fIseqall\fR\fR [\fB\-window\ \fR\fB\fIinteger\fR\fR] [\fB\-display\ \fR\fB\fIlist\fR\fR] \fB\-isdual\ \fR\fB\fIvariable\fR\fR \fB\-graph\ \fR\fB\fIxygraph\fR\fR \fB\-outfile\ \fR\fB\fIreport\fR\fR
+.HP \w'\fBdensity\fR\ 'u
+\fBdensity\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBdensity\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Composition" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-seqall\fR \fIseqall\fR
+.RS 4
+.RE
+.SS "Additional section"
+.PP
+\fB\-window\fR \fIinteger\fR
+.RS 4
+Default value: 100
+.RE
+.PP
+\fB\-display\fR \fIlist\fR
+.RS 4
+Default value: none
+.RE
+.SS "Output section"
+.PP
+\fB\-isdual\fR \fIvariable\fR
+.RS 4
+.RE
+.PP
+\fB\-graph\fR \fIxygraph\fR
+.RS 4
+.RE
+.PP
+\fB\-outfile\fR \fIreport\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+density is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/makeprotseq.1e
+++ emboss-6.4.0/debian/manpages/makeprotseq.1e
@@ -0,0 +1,97 @@
+'\" t
+.\"     Title: MAKEPROTSEQ
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "MAKEPROTSEQ" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+makeprotseq \- Create random protein sequences
+.SH "SYNOPSIS"
+.HP \w'\fBmakeprotseq\fR\ 'u
+\fBmakeprotseq\fR \fB\-pepstatsfile\ \fR\fB\fIinfile\fR\fR \fB\-amount\ \fR\fB\fIinteger\fR\fR \fB\-length\ \fR\fB\fIinteger\fR\fR [\fB\-useinsert\ \fR\fB\fItoggle\fR\fR] \fB\-insert\ \fR\fB\fIstring\fR\fR \fB\-start\ \fR\fB\fIinteger\fR\fR \fB\-makeseq\ \fR\fB\fIseqoutall\fR\fR
+.HP \w'\fBmakeprotseq\fR\ 'u
+\fBmakeprotseq\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBmakeprotseq\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-pepstatsfile\fR \fIinfile\fR
+.RS 4
+This file should be a pepstats output file\&. Protein sequences will be created with the composition in the pepstats output file\&.
+.RE
+.SS "Required section"
+.PP
+\fB\-amount\fR \fIinteger\fR
+.RS 4
+Default value: 100
+.RE
+.PP
+\fB\-length\fR \fIinteger\fR
+.RS 4
+Default value: 100
+.RE
+.PP
+\fB\-useinsert\fR \fItoggle\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-insert\fR \fIstring\fR
+.RS 4
+String that is inserted into sequence
+.RE
+.PP
+\fB\-start\fR \fIinteger\fR
+.RS 4
+Default value: 1
+.RE
+.SS "Output section"
+.PP
+\fB\-makeseq\fR \fIseqoutall\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+makeprotseq is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/pepnet.1e
+++ emboss-6.4.0/debian/manpages/pepnet.1e
@@ -0,0 +1,90 @@
+'\" t
+.\"     Title: PEPNET
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "PEPNET" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+pepnet \- Draw a helical net for a protein sequence
+.SH "SYNOPSIS"
+.HP \w'\fBpepnet\fR\ 'u
+\fBpepnet\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR \fB\-amphipathic\ \fR\fB\fItoggle\fR\fR \fB\-squares\ \fR\fB\fIstring\fR\fR \fB\-diamonds\ \fR\fB\fIstring\fR\fR \fB\-octags\ \fR\fB\fIstring\fR\fR \fB\-graph\ \fR\fB\fIgraph\fR\fR
+.HP \w'\fBpepnet\fR\ 'u
+\fBpepnet\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBpepnet\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Display,Protein:2D Structure" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIsequence\fR
+.RS 4
+.RE
+.SS "Output section"
+.PP
+\fB\-amphipathic\fR \fItoggle\fR
+.RS 4
+If this is true then the residues ACFGILMVWY are marked as squares and all other residues are unmarked\&. This overrides any other markup that you may have specified using the qualifiers \*(Aq\-squares\*(Aq, \*(Aq\-diamonds\*(Aq and \*(Aq\-octags\*(Aq\&.
+.RE
+.PP
+\fB\-squares\fR \fIstring\fR
+.RS 4
+By default the aliphatic residues ILVM are marked with squares\&. Default value: ILVM
+.RE
+.PP
+\fB\-diamonds\fR \fIstring\fR
+.RS 4
+By default the residues DENQST are marked with diamonds\&. Default value: DENQST
+.RE
+.PP
+\fB\-octags\fR \fIstring\fR
+.RS 4
+By default the positively charged residues HKR are marked with octagons\&. Default value: HKR
+.RE
+.PP
+\fB\-graph\fR \fIgraph\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+pepnet is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/pepwindowall.1e
+++ emboss-6.4.0/debian/manpages/pepwindowall.1e
@@ -0,0 +1,87 @@
+'\" t
+.\"     Title: PEPWINDOWALL
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "PEPWINDOWALL" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+pepwindowall \- Draw Kyte\-Doolittle hydropathy plot for a protein alignment
+.SH "SYNOPSIS"
+.HP \w'\fBpepwindowall\fR\ 'u
+\fBpepwindowall\fR \fB\-sequences\ \fR\fB\fIseqset\fR\fR [\fB\-datafile\ \fR\fB\fIdatafile\fR\fR] [\fB\-length\ \fR\fB\fIinteger\fR\fR] [\fB\-normalize\ \fR\fB\fIboolean\fR\fR] \fB\-graph\ \fR\fB\fIxygraph\fR\fR
+.HP \w'\fBpepwindowall\fR\ 'u
+\fBpepwindowall\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBpepwindowall\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Protein:Properties" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequences\fR \fIseqset\fR
+.RS 4
+File containing a sequence alignment
+.RE
+.PP
+\fB\-datafile\fR \fIdatafile\fR
+.RS 4
+Default value: Enakai\&.dat
+.RE
+.SS "Additional section"
+.PP
+\fB\-length\fR \fIinteger\fR
+.RS 4
+Default value: 19
+.RE
+.PP
+\fB\-normalize\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.SS "Output section"
+.PP
+\fB\-graph\fR \fIxygraph\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+pepwindowall is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/cacheensembl.1e
+++ emboss-6.4.0/debian/manpages/cacheensembl.1e
@@ -0,0 +1,76 @@
+'\" t
+.\"     Title: CACHEENSEMBL
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "CACHEENSEMBL" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+cacheensembl \- Generates server cache file for an Ensembl server
+.SH "SYNOPSIS"
+.HP \w'\fBcacheensembl\fR\ 'u
+\fBcacheensembl\fR \fB\-servername\ \fR\fB\fIstring\fR\fR [\fB\-outfile\ \fR\fB\fIoutfile\fR\fR] \fB\-cachefile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBcacheensembl\fR\ 'u
+\fBcacheensembl\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBcacheensembl\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Data resources" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-servername\fR \fIstring\fR
+.RS 4
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+Default value: stdout
+.RE
+.PP
+\fB\-cachefile\fR \fIoutfile\fR
+.RS 4
+Default value: server\&.$(servername)
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+cacheensembl is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/taxget.1e
+++ emboss-6.4.0/debian/manpages/taxget.1e
@@ -0,0 +1,72 @@
+'\" t
+.\"     Title: TAXGET
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "TAXGET" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+taxget \- Get taxon(s)
+.SH "SYNOPSIS"
+.HP \w'\fBtaxget\fR\ 'u
+\fBtaxget\fR \fB\-taxons\ \fR\fB\fItaxon\fR\fR \fB\-outfile\ \fR\fB\fIouttaxon\fR\fR
+.HP \w'\fBtaxget\fR\ 'u
+\fBtaxget\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBtaxget\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Ontology:Taxonomy" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-taxons\fR \fItaxon\fR
+.RS 4
+.RE
+.SS "Additional section"
+.SS "Advanced section"
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIouttaxon\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+taxget is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/prettyplot.1e
+++ emboss-6.4.0/debian/manpages/prettyplot.1e
@@ -0,0 +1,191 @@
+'\" t
+.\"     Title: PRETTYPLOT
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "PRETTYPLOT" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+prettyplot \- Draw a sequence alignment with pretty formatting
+.SH "SYNOPSIS"
+.HP \w'\fBprettyplot\fR\ 'u
+\fBprettyplot\fR \fB\-sequences\ \fR\fB\fIseqset\fR\fR [\fB\-matrixfile\ \fR\fB\fImatrix\fR\fR] [\fB\-residuesperline\ \fR\fB\fIinteger\fR\fR] [\fB\-resbreak\ \fR\fB\fIinteger\fR\fR] [\fB\-ccolours\ \fR\fB\fIboolean\fR\fR] [\fB\-cidentity\ \fR\fB\fIstring\fR\fR] [\fB\-csimilarity\ \fR\fB\fIstring\fR\fR] [\fB\-cother\ \fR\fB\fIstring\fR\fR] [\fB\-docolour\ \fR\fB\fIboolean\fR\fR] [\fB\-shade\ \fR\fB\fIstring\fR\fR] [\fB\-pair\ \fR\fB\fIarray\fR\fR] [\fB\-identity\ \fR\fB\fIinteger\fR\fR] [\fB\-box\ \fR\fB\fIboolean\fR\fR] [\fB\-boxcol\ \fR\fB\fIboolean\fR\fR] [\fB\-boxuse\ \fR\fB\fIstring\fR\fR] [\fB\-name\ \fR\fB\fIboolean\fR\fR] [\fB\-maxnamelen\ \fR\fB\fIinteger\fR\fR] [\fB\-number\ \fR\fB\fIboolean\fR\fR] [\fB\-listoptions\ \fR\fB\fIboolean\fR\fR] [\fB\-plurality\ \fR\fB\fIfloat\fR\fR] [\fB\-consensus\ \fR\fB\fIboolean\fR\fR] [\fB\-collision\ \fR\fB\fIboolean\fR\fR] [\fB\-alternative\ \fR\fB\fIlist\fR\fR] [\fB\-showscore\ \fR\fB\fIinteger\fR\fR] [\fB\-portrait\ \fR\fB\fIboolean\fR\fR] \fB\-graph\ \fR\fB\fIgraph\fR\fR
+.HP \w'\fBprettyplot\fR\ 'u
+\fBprettyplot\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBprettyplot\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Alignment:Multiple,Display" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequences\fR \fIseqset\fR
+.RS 4
+.RE
+.PP
+\fB\-matrixfile\fR \fImatrix\fR
+.RS 4
+This is the scoring matrix file used when comparing sequences\&. By default it is the file \*(AqEBLOSUM62\*(Aq (for proteins) or the file \*(AqEDNAFULL\*(Aq (for nucleic sequences)\&. These files are found in the \*(Aqdata\*(Aq directory of the EMBOSS installation\&.
+.RE
+.SS "Additional section"
+.PP
+\fB\-residuesperline\fR \fIinteger\fR
+.RS 4
+The number of residues to be displayed on each line Default value: 50
+.RE
+.PP
+\fB\-resbreak\fR \fIinteger\fR
+.RS 4
+Default value: $(residuesperline)
+.RE
+.PP
+\fB\-ccolours\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-cidentity\fR \fIstring\fR
+.RS 4
+Default value: RED
+.RE
+.PP
+\fB\-csimilarity\fR \fIstring\fR
+.RS 4
+Default value: GREEN
+.RE
+.PP
+\fB\-cother\fR \fIstring\fR
+.RS 4
+Default value: BLACK
+.RE
+.PP
+\fB\-docolour\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-shade\fR \fIstring\fR
+.RS 4
+Set to BPLW for normal shading (black, pale, light, white) so for pair = 1\&.5,1\&.0,0\&.5 and shade = BPLW Residues score Colour 1\&.5 or over\&.\&.\&. BLACK (B) 1\&.0 to 1\&.5 \&.\&.\&. BROWN (P) 0\&.5 to 1\&.0 \&.\&.\&. WHEAT (L) under 0\&.5 \&.\&.\&.\&. WHITE (W) The only four letters allowed are BPLW, in any order\&.
+.RE
+.PP
+\fB\-pair\fR \fIarray\fR
+.RS 4
+Default value: 1\&.5,1\&.0,0\&.5
+.RE
+.PP
+\fB\-identity\fR \fIinteger\fR
+.RS 4
+.RE
+.PP
+\fB\-box\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-boxcol\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-boxuse\fR \fIstring\fR
+.RS 4
+Default value: GREY
+.RE
+.PP
+\fB\-name\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-maxnamelen\fR \fIinteger\fR
+.RS 4
+Default value: 10
+.RE
+.PP
+\fB\-number\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-listoptions\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-plurality\fR \fIfloat\fR
+.RS 4
+Default value: @( $(sequences\&.totweight) / 2)
+.RE
+.SS "Consensus section"
+.PP
+\fB\-consensus\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-collision\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-alternative\fR \fIlist\fR
+.RS 4
+Values are 0:Normal collision check\&. (default) 1:Compares identical scores with the max score found\&. So if any other residue matches the identical score then a collision has occurred\&. 2:If another residue has a greater than or equal to matching score and these do not match then a collision has occurred\&. 3:Checks all those not in the current consensus\&.If any of these give a top score for matching or identical scores then a collision has occured\&.
+.RE
+.PP
+\fB\-showscore\fR \fIinteger\fR
+.RS 4
+Default value: \-1
+.RE
+.PP
+\fB\-portrait\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.SS "Output section"
+.PP
+\fB\-graph\fR \fIgraph\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+prettyplot is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/banana.1e
+++ emboss-6.4.0/debian/manpages/banana.1e
@@ -0,0 +1,85 @@
+'\" t
+.\"     Title: BANANA
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "BANANA" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+banana \- Plot bending and curvature data for B\-DNA
+.SH "SYNOPSIS"
+.HP \w'\fBbanana\fR\ 'u
+\fBbanana\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR [\fB\-anglesfile\ \fR\fB\fIdatafile\fR\fR] \fB\-graph\ \fR\fB\fIgraph\fR\fR [\fB\-residuesperline\ \fR\fB\fIinteger\fR\fR] [\fB\-outfile\ \fR\fB\fIoutfile\fR\fR]
+.HP \w'\fBbanana\fR\ 'u
+\fBbanana\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBbanana\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Properties,Nucleic:Composition,Nucleic:2D structure" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIsequence\fR
+.RS 4
+.RE
+.PP
+\fB\-anglesfile\fR \fIdatafile\fR
+.RS 4
+Default value: Eangles_tri\&.dat
+.RE
+.SS "Output section"
+.PP
+\fB\-graph\fR \fIgraph\fR
+.RS 4
+.RE
+.PP
+\fB\-residuesperline\fR \fIinteger\fR
+.RS 4
+Default value: 50
+.RE
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+Default value: banana\&.profile
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+banana is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/tfextract.1e
+++ emboss-6.4.0/debian/manpages/tfextract.1e
@@ -0,0 +1,65 @@
+'\" t
+.\"     Title: TFEXTRACT
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "TFEXTRACT" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+tfextract \- Process TRANSFAC transcription factor database for use by tfscan
+.SH "SYNOPSIS"
+.HP \w'\fBtfextract\fR\ 'u
+\fBtfextract\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR
+.HP \w'\fBtfextract\fR\ 'u
+\fBtfextract\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBtfextract\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Database creation" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-infile\fR \fIinfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+tfextract is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/pepstats.1e
+++ emboss-6.4.0/debian/manpages/pepstats.1e
@@ -0,0 +1,91 @@
+'\" t
+.\"     Title: PEPSTATS
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "PEPSTATS" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+pepstats \- Calculates statistics of protein properties
+.SH "SYNOPSIS"
+.HP \w'\fBpepstats\fR\ 'u
+\fBpepstats\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-aadata\ \fR\fB\fIdatafile\fR\fR \fB\-mwdata\ \fR\fB\fIdatafile\fR\fR \fB\-termini\ \fR\fB\fIboolean\fR\fR \fB\-mono\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBpepstats\fR\ 'u
+\fBpepstats\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBpepstats\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Protein:Composition,Protein:Properties" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqall\fR
+.RS 4
+.RE
+.PP
+\fB\-aadata\fR \fIdatafile\fR
+.RS 4
+Amino acid properties Default value: Eamino\&.dat
+.RE
+.PP
+\fB\-mwdata\fR \fIdatafile\fR
+.RS 4
+Molecular weight data for amino acids Default value: Emolwt\&.dat
+.RE
+.SS "Advanced section"
+.PP
+\fB\-termini\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-mono\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+pepstats is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/xmltoxml.1e
+++ emboss-6.4.0/debian/manpages/xmltoxml.1e
@@ -0,0 +1,93 @@
+'\" t
+.\"     Title: XMLTOXML
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "XMLTOXML" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+xmltoxml \- Convert an XML document to a different format
+.SH "SYNOPSIS"
+.HP \w'\fBxmltoxml\fR\ 'u
+\fBxmltoxml\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR \fB\-type\ \fR\fB\fIlist\fR\fR \fB\-seq\ \fR\fB\fIlist\fR\fR \fB\-feat\ \fR\fB\fIlist\fR\fR \fB\-align\ \fR\fB\fIlist\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBxmltoxml\fR\ 'u
+\fBxmltoxml\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBxmltoxml\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Misc" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-infile\fR \fIinfile\fR
+.RS 4
+.RE
+.SS "Required section"
+.PP
+\fB\-type\fR \fIlist\fR
+.RS 4
+You must specify the type of file content so that appropriate output format options may be generated\&.
+.RE
+.PP
+\fB\-seq\fR \fIlist\fR
+.RS 4
+This option sets the XML format of a sequence output file\&. Default value: X
+.RE
+.PP
+\fB\-feat\fR \fIlist\fR
+.RS 4
+This option sets the XML format of a sequence feature output file\&. Default value: X
+.RE
+.PP
+\fB\-align\fR \fIlist\fR
+.RS 4
+This option sets the XML format of a sequence alignment output file\&. Default value: X
+.RE
+.SS "Additional section"
+.SS "Advanced section"
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+xmltoxml is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/primersearch.1e
+++ emboss-6.4.0/debian/manpages/primersearch.1e
@@ -0,0 +1,79 @@
+'\" t
+.\"     Title: PRIMERSEARCH
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "PRIMERSEARCH" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+primersearch \- Search DNA sequences for matches with primer pairs
+.SH "SYNOPSIS"
+.HP \w'\fBprimersearch\fR\ 'u
+\fBprimersearch\fR \fB\-seqall\ \fR\fB\fIseqall\fR\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR \fB\-mismatchpercent\ \fR\fB\fIinteger\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBprimersearch\fR\ 'u
+\fBprimersearch\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBprimersearch\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Primers" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-seqall\fR \fIseqall\fR
+.RS 4
+.RE
+.PP
+\fB\-infile\fR \fIinfile\fR
+.RS 4
+.RE
+.SS "Required section"
+.PP
+\fB\-mismatchpercent\fR \fIinteger\fR
+.RS 4
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+primersearch is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/showdb.1e
+++ emboss-6.4.0/debian/manpages/showdb.1e
@@ -0,0 +1,183 @@
+'\" t
+.\"     Title: SHOWDB
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "SHOWDB" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+showdb \- Displays information on configured databases
+.SH "SYNOPSIS"
+.HP \w'\fBshowdb\fR\ 'u
+\fBshowdb\fR [\fB\-database\ \fR\fB\fIstring\fR\fR] [\fB\-html\ \fR\fB\fIboolean\fR\fR] [\fB\-protein\ \fR\fB\fIboolean\fR\fR] [\fB\-nucleic\ \fR\fB\fIboolean\fR\fR] [\fB\-sequence\ \fR\fB\fIboolean\fR\fR] [\fB\-feature\ \fR\fB\fIboolean\fR\fR] [\fB\-text\ \fR\fB\fIboolean\fR\fR] [\fB\-taxonomy\ \fR\fB\fIboolean\fR\fR] [\fB\-resource\ \fR\fB\fIboolean\fR\fR] [\fB\-assembly\ \fR\fB\fIboolean\fR\fR] [\fB\-obo\ \fR\fB\fIboolean\fR\fR] [\fB\-full\ \fR\fB\fIboolean\fR\fR] [\fB\-methods\ \fR\fB\fIboolean\fR\fR] [\fB\-fields\ \fR\fB\fIboolean\fR\fR] [\fB\-defined\ \fR\fB\fIboolean\fR\fR] [\fB\-release\ \fR\fB\fIboolean\fR\fR] \fB\-only\ \fR\fB\fItoggle\fR\fR \fB\-heading\ \fR\fB\fIboolean\fR\fR \fB\-type\ \fR\fB\fIboolean\fR\fR \fB\-id\ \fR\fB\fIboolean\fR\fR \fB\-query\ \fR\fB\fIboolean\fR\fR \fB\-all\ \fR\fB\fIboolean\fR\fR \fB\-comment\ \fR\fB\fIboolean\fR\fR [\fB\-outfile\ \fR\fB\fIoutfile\fR\fR]
+.HP \w'\fBshowdb\fR\ 'u
+\fBshowdb\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBshowdb\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Data resources" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-database\fR \fIstring\fR
+.RS 4
+.RE
+.SS "Additional section"
+.PP
+\fB\-html\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-protein\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-nucleic\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-sequence\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-feature\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-text\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-taxonomy\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-resource\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-assembly\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-obo\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-full\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-methods\fR \fIboolean\fR
+.RS 4
+This displays the access methods that can be used on this database, for all, query or ID access Default value: $(full)
+.RE
+.PP
+\fB\-fields\fR \fIboolean\fR
+.RS 4
+This displays the search fields that can be used on this database, other than the standard \*(Aqid\*(Aq or \*(Aqacc\*(Aq fields\&. Default value: $(full)
+.RE
+.PP
+\fB\-defined\fR \fIboolean\fR
+.RS 4
+This displays a short name for the file containing the database definition Default value: $(full)
+.RE
+.PP
+\fB\-release\fR \fIboolean\fR
+.RS 4
+Default value: $(full)
+.RE
+.SS "Advanced section"
+.PP
+\fB\-only\fR \fItoggle\fR
+.RS 4
+This is a way of shortening the command line if you only want a few standard columns to be displayed\&. Instead of specifying: \*(Aq\-nohead \-notype \-noid \-noquery \-noall\*(Aq to get only the comment output, you can specify \*(Aq\-only \-comment\*(Aq Default value: N
+.RE
+.PP
+\fB\-heading\fR \fIboolean\fR
+.RS 4
+Default value: @(!$(only))
+.RE
+.PP
+\fB\-type\fR \fIboolean\fR
+.RS 4
+Default value: @(!$(only))
+.RE
+.PP
+\fB\-id\fR \fIboolean\fR
+.RS 4
+Default value: @(!$(only))
+.RE
+.PP
+\fB\-query\fR \fIboolean\fR
+.RS 4
+Default value: @(!$(only))
+.RE
+.PP
+\fB\-all\fR \fIboolean\fR
+.RS 4
+Default value: @(!$(only))
+.RE
+.PP
+\fB\-comment\fR \fIboolean\fR
+.RS 4
+Default value: @(!$(only))
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+Default value: stdout
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+showdb is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/embossversion.1e
+++ emboss-6.4.0/debian/manpages/embossversion.1e
@@ -0,0 +1,71 @@
+'\" t
+.\"     Title: EMBOSSVERSION
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "EMBOSSVERSION" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+embossversion \- Reports the current EMBOSS version number
+.SH "SYNOPSIS"
+.HP \w'\fBembossversion\fR\ 'u
+\fBembossversion\fR [\fB\-full\ \fR\fB\fIboolean\fR\fR] [\fB\-outfile\ \fR\fB\fIoutfile\fR\fR]
+.HP \w'\fBembossversion\fR\ 'u
+\fBembossversion\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBembossversion\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils" command group(s)\&.
+.SH "OPTIONS"
+.SS "Additional section"
+.PP
+\fB\-full\fR \fIboolean\fR
+.RS 4
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+Default value: stdout
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+embossversion is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/cusp.1e
+++ emboss-6.4.0/debian/manpages/cusp.1e
@@ -0,0 +1,70 @@
+'\" t
+.\"     Title: CUSP
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "CUSP" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+cusp \- Create a codon usage table from nucleotide sequence(s)
+.SH "SYNOPSIS"
+.HP \w'\fBcusp\fR\ 'u
+\fBcusp\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBcusp\fR\ 'u
+\fBcusp\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBcusp\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Codon usage" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqall\fR
+.RS 4
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+cusp is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/urlget.1e
+++ emboss-6.4.0/debian/manpages/urlget.1e
@@ -0,0 +1,72 @@
+'\" t
+.\"     Title: URLGET
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "URLGET" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+urlget \- Get URLs of data resources
+.SH "SYNOPSIS"
+.HP \w'\fBurlget\fR\ 'u
+\fBurlget\fR \fB\-url\ \fR\fB\fIurl\fR\fR \fB\-outfile\ \fR\fB\fIouturl\fR\fR
+.HP \w'\fBurlget\fR\ 'u
+\fBurlget\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBurlget\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Data retrieval:Url data" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-url\fR \fIurl\fR
+.RS 4
+.RE
+.SS "Additional section"
+.SS "Advanced section"
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIouturl\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+urlget is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/distmat.1e
+++ emboss-6.4.0/debian/manpages/distmat.1e
@@ -0,0 +1,108 @@
+'\" t
+.\"     Title: DISTMAT
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "DISTMAT" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+distmat \- Create a distance matrix from a multiple sequence alignment
+.SH "SYNOPSIS"
+.HP \w'\fBdistmat\fR\ 'u
+\fBdistmat\fR \fB\-sequence\ \fR\fB\fIseqset\fR\fR \fB\-nucmethod\ \fR\fB\fIlist\fR\fR \fB\-protmethod\ \fR\fB\fIlist\fR\fR \fB\-ambiguous\ \fR\fB\fIboolean\fR\fR \fB\-gapweight\ \fR\fB\fIfloat\fR\fR \fB\-position\ \fR\fB\fIinteger\fR\fR \fB\-calculatea\ \fR\fB\fIboolean\fR\fR \fB\-parametera\ \fR\fB\fIfloat\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBdistmat\fR\ 'u
+\fBdistmat\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBdistmat\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Molecular sequence" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqset\fR
+.RS 4
+File containing a sequence alignment\&.
+.RE
+.SS "Required section"
+.PP
+\fB\-nucmethod\fR \fIlist\fR
+.RS 4
+Multiple substitution correction methods for nucleotides\&.
+.RE
+.PP
+\fB\-protmethod\fR \fIlist\fR
+.RS 4
+Multiple substitution correction methods for proteins\&.
+.RE
+.SS "Additional section"
+.PP
+\fB\-ambiguous\fR \fIboolean\fR
+.RS 4
+Option to use the ambiguous codes in the calculation of the Jukes\-Cantor method or if the sequences are proteins\&. Default value: N
+.RE
+.PP
+\fB\-gapweight\fR \fIfloat\fR
+.RS 4
+Option to weight gaps in the uncorrected (nucleotide) and Jukes\-Cantor distance methods\&. Default value: 0\&.
+.RE
+.PP
+\fB\-position\fR \fIinteger\fR
+.RS 4
+Choose base positions to analyse in each codon i\&.e\&. 123 (all bases), 12 (the first two bases), 1, 2, or 3 individual bases\&. Default value: 123
+.RE
+.PP
+\fB\-calculatea\fR \fIboolean\fR
+.RS 4
+This will force the calculation of parameter \*(Aqa\*(Aq in the Jin\-Nei Gamma distance calculation, otherwise the default is 1\&.0 (see \-parametera option)\&. Default value: N
+.RE
+.PP
+\fB\-parametera\fR \fIfloat\fR
+.RS 4
+User defined parameter \*(Aqa\*(Aq to be use in the Jin\-Nei Gamma distance calculation\&. The suggested value to be used is 1\&.0 (Jin et al\&.) and this is the default\&. Default value: 1\&.0
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+distmat is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/syco.1e
+++ emboss-6.4.0/debian/manpages/syco.1e
@@ -0,0 +1,100 @@
+'\" t
+.\"     Title: SYCO
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "SYCO" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+syco \- Draw synonymous codon usage statistic plot for a nucleotide sequence
+.SH "SYNOPSIS"
+.HP \w'\fBsyco\fR\ 'u
+\fBsyco\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR \fB\-cfile\ \fR\fB\fIcodon\fR\fR \fB\-window\ \fR\fB\fIinteger\fR\fR \fB\-uncommon\ \fR\fB\fIboolean\fR\fR \fB\-minimum\ \fR\fB\fIfloat\fR\fR \fB\-plot\ \fR\fB\fItoggle\fR\fR \fB\-graph\ \fR\fB\fIxygraph\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBsyco\fR\ 'u
+\fBsyco\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBsyco\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Codon usage,Nucleic:Gene finding" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIsequence\fR
+.RS 4
+.RE
+.PP
+\fB\-cfile\fR \fIcodon\fR
+.RS 4
+Codon usage file
+.RE
+.SS "Advanced section"
+.PP
+\fB\-window\fR \fIinteger\fR
+.RS 4
+Default value: 30
+.RE
+.PP
+\fB\-uncommon\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-minimum\fR \fIfloat\fR
+.RS 4
+Default value: \&.15
+.RE
+.SS "Output section"
+.PP
+\fB\-plot\fR \fItoggle\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-graph\fR \fIxygraph\fR
+.RS 4
+.RE
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+syco is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/edamisid.1e
+++ emboss-6.4.0/debian/manpages/edamisid.1e
@@ -0,0 +1,92 @@
+'\" t
+.\"     Title: EDAMISID
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "EDAMISID" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+edamisid \- Find EDAM ontology terms by is_identifier_of relation
+.SH "SYNOPSIS"
+.HP \w'\fBedamisid\fR\ 'u
+\fBedamisid\fR \fB\-identifier\ \fR\fB\fIstring\fR\fR [\fB\-namespace\ \fR\fB\fIlist\fR\fR] \fB\-sensitive\ \fR\fB\fIboolean\fR\fR \fB\-subclasses\ \fR\fB\fIboolean\fR\fR \fB\-obsolete\ \fR\fB\fIboolean\fR\fR \fB\-edamisid\ \fR\fB\fIoutobo\fR\fR
+.HP \w'\fBedamisid\fR\ 'u
+\fBedamisid\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBedamisid\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Ontology:EDAM,Data retrieval:Ontology data" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-identifier\fR \fIstring\fR
+.RS 4
+.RE
+.SS "Additional section"
+.PP
+\fB\-namespace\fR \fIlist\fR
+.RS 4
+By default all terms are returned\&. Searches can be limited to one or a few namespaces\&. Default value: *
+.RE
+.SS "Advanced section"
+.PP
+\fB\-sensitive\fR \fIboolean\fR
+.RS 4
+By default, the query keywords are matched against the EDAM term names (and synonyms) only\&. This option also matches the keywords against the EDAM term definitions and will therefore (typically) report more matches\&. Default value: N
+.RE
+.PP
+\fB\-subclasses\fR \fIboolean\fR
+.RS 4
+Extend the query matches to include all terms which are specialisations (EDAM sub\-classes) of the matched type\&. Default value: N
+.RE
+.PP
+\fB\-obsolete\fR \fIboolean\fR
+.RS 4
+The default behaviour is to not use or return obsolete terms\&. This option if set will include all terms\&. Default value: N
+.RE
+.SS "Output section"
+.PP
+\fB\-edamisid\fR \fIoutobo\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+edamisid is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/chaos.1e
+++ emboss-6.4.0/debian/manpages/chaos.1e
@@ -0,0 +1,70 @@
+'\" t
+.\"     Title: CHAOS
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "CHAOS" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+chaos \- Draw a chaos game representation plot for a nucleotide sequence
+.SH "SYNOPSIS"
+.HP \w'\fBchaos\fR\ 'u
+\fBchaos\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR \fB\-graph\ \fR\fB\fIgraph\fR\fR
+.HP \w'\fBchaos\fR\ 'u
+\fBchaos\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBchaos\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Composition" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIsequence\fR
+.RS 4
+.RE
+.SS "Output section"
+.PP
+\fB\-graph\fR \fIgraph\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+chaos is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/cachedbfetch.1e
+++ emboss-6.4.0/debian/manpages/cachedbfetch.1e
@@ -0,0 +1,77 @@
+'\" t
+.\"     Title: CACHEDBFETCH
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "CACHEDBFETCH" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+cachedbfetch \- Generates server cache file for Dbfetch/WSDbfetch data sources
+.SH "SYNOPSIS"
+.HP \w'\fBcachedbfetch\fR\ 'u
+\fBcachedbfetch\fR \fB\-servername\ \fR\fB\fIstring\fR\fR [\fB\-outfile\ \fR\fB\fIoutfile\fR\fR] \fB\-cachefile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBcachedbfetch\fR\ 'u
+\fBcachedbfetch\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBcachedbfetch\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Data resources" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-servername\fR \fIstring\fR
+.RS 4
+Default value: dbfetch
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+Default value: stdout
+.RE
+.PP
+\fB\-cachefile\fR \fIoutfile\fR
+.RS 4
+Default value: server\&.$(servername)
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+cachedbfetch is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/seqinfo.1e
+++ emboss-6.4.0/debian/manpages/seqinfo.1e
@@ -0,0 +1,71 @@
+'\" t
+.\"     Title: SEQINFO
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "SEQINFO" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+seqinfo \- Returns sequence information
+.SH "SYNOPSIS"
+.HP \w'\fBseqinfo\fR\ 'u
+\fBseqinfo\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBseqinfo\fR\ 'u
+\fBseqinfo\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBseqinfo\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Test" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqall\fR
+.RS 4
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+Default value: stdout
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+seqinfo is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/dbxfasta.1e
+++ emboss-6.4.0/debian/manpages/dbxfasta.1e
@@ -0,0 +1,120 @@
+'\" t
+.\"     Title: DBXFASTA
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "DBXFASTA" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+dbxfasta \- Index a fasta file database using b+tree indices
+.SH "SYNOPSIS"
+.HP \w'\fBdbxfasta\fR\ 'u
+\fBdbxfasta\fR \fB\-dbname\ \fR\fB\fIstring\fR\fR \fB\-dbresource\ \fR\fB\fIstring\fR\fR \fB\-idformat\ \fR\fB\fIlist\fR\fR \fB\-directory\ \fR\fB\fIdirectory\fR\fR \fB\-filenames\ \fR\fB\fIstring\fR\fR \fB\-fields\ \fR\fB\fIlist\fR\fR \fB\-compressed\ \fR\fB\fIboolean\fR\fR \fB\-release\ \fR\fB\fIstring\fR\fR \fB\-date\ \fR\fB\fIstring\fR\fR \fB\-exclude\ \fR\fB\fIstring\fR\fR \fB\-indexoutdir\ \fR\fB\fIoutdir\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBdbxfasta\fR\ 'u
+\fBdbxfasta\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBdbxfasta\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Database indexing" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-dbname\fR \fIstring\fR
+.RS 4
+.RE
+.PP
+\fB\-dbresource\fR \fIstring\fR
+.RS 4
+.RE
+.PP
+\fB\-idformat\fR \fIlist\fR
+.RS 4
+Default value: idacc
+.RE
+.PP
+\fB\-directory\fR \fIdirectory\fR
+.RS 4
+Default value: \&.
+.RE
+.PP
+\fB\-filenames\fR \fIstring\fR
+.RS 4
+Default value: *\&.fasta
+.RE
+.SS "Required section"
+.PP
+\fB\-fields\fR \fIlist\fR
+.RS 4
+Default value: id,acc
+.RE
+.PP
+\fB\-compressed\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.SS "Advanced section"
+.PP
+\fB\-release\fR \fIstring\fR
+.RS 4
+Default value: 0\&.0
+.RE
+.PP
+\fB\-date\fR \fIstring\fR
+.RS 4
+Default value: 00/00/00
+.RE
+.PP
+\fB\-exclude\fR \fIstring\fR
+.RS 4
+.RE
+.SS "Output section"
+.PP
+\fB\-indexoutdir\fR \fIoutdir\fR
+.RS 4
+Default value: \&.
+.RE
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+dbxfasta is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/tfm.1e
+++ emboss-6.4.0/debian/manpages/tfm.1e
@@ -0,0 +1,82 @@
+'\" t
+.\"     Title: TFM
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "TFM" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+tfm \- Displays full documentation for an application
+.SH "SYNOPSIS"
+.HP \w'\fBtfm\fR\ 'u
+\fBtfm\fR \fB\-program\ \fR\fB\fIstring\fR\fR [\fB\-outfile\ \fR\fB\fIoutfile\fR\fR] [\fB\-html\ \fR\fB\fIboolean\fR\fR] [\fB\-more\ \fR\fB\fIboolean\fR\fR]
+.HP \w'\fBtfm\fR\ 'u
+\fBtfm\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBtfm\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Documentation" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-program\fR \fIstring\fR
+.RS 4
+Enter the name of an EMBOSS program
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+Default value: stdout
+.RE
+.PP
+\fB\-html\fR \fIboolean\fR
+.RS 4
+This will format the output for displaying as a WWW document\&. Default value: N
+.RE
+.PP
+\fB\-more\fR \fIboolean\fR
+.RS 4
+This uses the standard UNIX utility \*(Aqmore\*(Aq to display the text page\-by\-page, waiting for you to read one screen\-full before going on to the next page\&. When you have finished reading a page, press the SPACE bar to proceed to the next page\&. Default value: @(!$(html))
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+tfm is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/needle.1e
+++ emboss-6.4.0/debian/manpages/needle.1e
@@ -0,0 +1,111 @@
+'\" t
+.\"     Title: NEEDLE
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "NEEDLE" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+needle \- Needleman\-Wunsch global alignment of two sequences
+.SH "SYNOPSIS"
+.HP \w'\fBneedle\fR\ 'u
+\fBneedle\fR \fB\-asequence\ \fR\fB\fIsequence\fR\fR \fB\-bsequence\ \fR\fB\fIseqall\fR\fR [\fB\-datafile\ \fR\fB\fImatrixf\fR\fR] \fB\-gapopen\ \fR\fB\fIfloat\fR\fR \fB\-gapextend\ \fR\fB\fIfloat\fR\fR [\fB\-endweight\ \fR\fB\fIboolean\fR\fR] [\fB\-endopen\ \fR\fB\fIfloat\fR\fR] [\fB\-endextend\ \fR\fB\fIfloat\fR\fR] \fB\-brief\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIalign\fR\fR
+.HP \w'\fBneedle\fR\ 'u
+\fBneedle\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBneedle\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Alignment:Global" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-asequence\fR \fIsequence\fR
+.RS 4
+.RE
+.PP
+\fB\-bsequence\fR \fIseqall\fR
+.RS 4
+.RE
+.PP
+\fB\-datafile\fR \fImatrixf\fR
+.RS 4
+This is the scoring matrix file used when comparing sequences\&. By default it is the file \*(AqEBLOSUM62\*(Aq (for proteins) or the file \*(AqEDNAFULL\*(Aq (for nucleic sequences)\&. These files are found in the \*(Aqdata\*(Aq directory of the EMBOSS installation\&.
+.RE
+.SS "Required section"
+.PP
+\fB\-gapopen\fR \fIfloat\fR
+.RS 4
+The gap open penalty is the score taken away when a gap is created\&. The best value depends on the choice of comparison matrix\&. The default value assumes you are using the EBLOSUM62 matrix for protein sequences, and the EDNAFULL matrix for nucleotide sequences\&. Default value: @($(acdprotein)? 10\&.0 : 10\&.0 )
+.RE
+.PP
+\fB\-gapextend\fR \fIfloat\fR
+.RS 4
+The gap extension, penalty is added to the standard gap penalty for each base or residue in the gap\&. This is how long gaps are penalized\&. Usually you will expect a few long gaps rather than many short gaps, so the gap extension penalty should be lower than the gap penalty\&. An exception is where one or both sequences are single reads with possible sequencing errors in which case you would expect many single base gaps\&. You can get this result by setting the gap open penalty to zero (or very low) and using the gap extension penalty to control gap scoring\&. Default value: @($(acdprotein)? 0\&.5 : 0\&.5 )
+.RE
+.SS "Additional section"
+.PP
+\fB\-endweight\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-endopen\fR \fIfloat\fR
+.RS 4
+The end gap open penalty is the score taken away when an end gap is created\&. The best value depends on the choice of comparison matrix\&. The default value assumes you are using the EBLOSUM62 matrix for protein sequences, and the EDNAFULL matrix for nucleotide sequences\&. Default value: @($(acdprotein)? 10\&.0 : 10\&.0 )
+.RE
+.PP
+\fB\-endextend\fR \fIfloat\fR
+.RS 4
+The end gap extension, penalty is added to the end gap penalty for each base or residue in the end gap\&. This is how long end gaps are penalized\&. Default value: @($(acdprotein)? 0\&.5 : 0\&.5 )
+.RE
+.SS "Output section"
+.PP
+\fB\-brief\fR \fIboolean\fR
+.RS 4
+Brief identity and similarity Default value: Y
+.RE
+.PP
+\fB\-outfile\fR \fIalign\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+needle is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/skipseq.1e
+++ emboss-6.4.0/debian/manpages/skipseq.1e
@@ -0,0 +1,78 @@
+'\" t
+.\"     Title: SKIPSEQ
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "SKIPSEQ" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+skipseq \- Reads and writes (returns) sequences, skipping first few
+.SH "SYNOPSIS"
+.HP \w'\fBskipseq\fR\ 'u
+\fBskipseq\fR \fB\-feature\ \fR\fB\fIboolean\fR\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-skip\ \fR\fB\fIinteger\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR
+.HP \w'\fBskipseq\fR\ 'u
+\fBskipseq\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBskipseq\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-feature\fR \fIboolean\fR
+.RS 4
+.RE
+.PP
+\fB\-sequence\fR \fIseqall\fR
+.RS 4
+.RE
+.PP
+\fB\-skip\fR \fIinteger\fR
+.RS 4
+.RE
+.SS "Output section"
+.PP
+\fB\-outseq\fR \fIseqoutall\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+skipseq is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/makenucseq.1e
+++ emboss-6.4.0/debian/manpages/makenucseq.1e
@@ -0,0 +1,97 @@
+'\" t
+.\"     Title: MAKENUCSEQ
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "MAKENUCSEQ" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+makenucseq \- Create random nucleotide sequences
+.SH "SYNOPSIS"
+.HP \w'\fBmakenucseq\fR\ 'u
+\fBmakenucseq\fR \fB\-codonfile\ \fR\fB\fIcodon\fR\fR \fB\-amount\ \fR\fB\fIinteger\fR\fR \fB\-length\ \fR\fB\fIinteger\fR\fR [\fB\-useinsert\ \fR\fB\fItoggle\fR\fR] \fB\-insert\ \fR\fB\fIstring\fR\fR \fB\-start\ \fR\fB\fIinteger\fR\fR \fB\-makeseq\ \fR\fB\fIseqoutall\fR\fR
+.HP \w'\fBmakenucseq\fR\ 'u
+\fBmakenucseq\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBmakenucseq\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-codonfile\fR \fIcodon\fR
+.RS 4
+Optional codon usage file\&. Nucleotide sequences will be created as triplets matching the frequencies in the file, with the end trimmed to be in the correct reading frame\&.
+.RE
+.SS "Required section"
+.PP
+\fB\-amount\fR \fIinteger\fR
+.RS 4
+Default value: 100
+.RE
+.PP
+\fB\-length\fR \fIinteger\fR
+.RS 4
+Default value: 100
+.RE
+.PP
+\fB\-useinsert\fR \fItoggle\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-insert\fR \fIstring\fR
+.RS 4
+String that is inserted into sequence
+.RE
+.PP
+\fB\-start\fR \fIinteger\fR
+.RS 4
+Default value: 1
+.RE
+.SS "Output section"
+.PP
+\fB\-makeseq\fR \fIseqoutall\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+makenucseq is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/fuzznuc.1e
+++ emboss-6.4.0/debian/manpages/fuzznuc.1e
@@ -0,0 +1,81 @@
+'\" t
+.\"     Title: FUZZNUC
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "FUZZNUC" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+fuzznuc \- Search for patterns in nucleotide sequences
+.SH "SYNOPSIS"
+.HP \w'\fBfuzznuc\fR\ 'u
+\fBfuzznuc\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-pattern\ \fR\fB\fIpattern\fR\fR \fB\-complement\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIreport\fR\fR
+.HP \w'\fBfuzznuc\fR\ 'u
+\fBfuzznuc\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBfuzznuc\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Motifs" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqall\fR
+.RS 4
+.RE
+.PP
+\fB\-pattern\fR \fIpattern\fR
+.RS 4
+The standard IUPAC one\-letter codes for the nucleotides are used\&. The symbol \*(Aqn\*(Aq is used for a position where any nucleotide is accepted\&. Ambiguities are indicated by listing the acceptable nucleotides for a given position, between square parentheses \*(Aq[ ]\*(Aq\&. For example: [ACG] stands for A or C or G\&. Ambiguities are also indicated by listing between a pair of curly brackets \*(Aq{ }\*(Aq the nucleotides that are not accepted at a given position\&. For example: {AG} stands for any nucleotides except A and G\&. Each element in a pattern is separated from its neighbor by a \*(Aq\-\*(Aq\&. (Optional in fuzznuc)\&. Repetition of an element of the pattern can be indicated by following that element with a numerical value or a numerical range between parenthesis\&. Examples: N(3) corresponds to N\-N\-N, N(2,4) corresponds to N\-N or N\-N\-N or N\-N\-N\-N\&. When a pattern is restricted to either the 5\*(Aq or 3\*(Aq end of a sequence, that pattern either starts with a \*(Aq<\*(Aq symbol or respectively ends with a \*(Aq>\*(Aq symbol\&. A period ends the pattern\&. (Optional in fuzznuc)\&. For example, [CG](5)TG{A}N(1,5)C
+.RE
+.SS "Advanced section"
+.PP
+\fB\-complement\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIreport\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+fuzznuc is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/mwcontam.1e
+++ emboss-6.4.0/debian/manpages/mwcontam.1e
@@ -0,0 +1,76 @@
+'\" t
+.\"     Title: MWCONTAM
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "MWCONTAM" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+mwcontam \- Find weights common to multiple molecular weights files
+.SH "SYNOPSIS"
+.HP \w'\fBmwcontam\fR\ 'u
+\fBmwcontam\fR \fB\-files\ \fR\fB\fIfilelist\fR\fR \fB\-tolerance\ \fR\fB\fIfloat\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBmwcontam\fR\ 'u
+\fBmwcontam\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBmwcontam\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Protein:Composition" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-files\fR \fIfilelist\fR
+.RS 4
+.RE
+.SS "Required section"
+.PP
+\fB\-tolerance\fR \fIfloat\fR
+.RS 4
+Default value: 50\&.0
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+mwcontam is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/listor.1e
+++ emboss-6.4.0/debian/manpages/listor.1e
@@ -0,0 +1,81 @@
+'\" t
+.\"     Title: LISTOR
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "LISTOR" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+listor \- Write a list file of the logical OR of two sets of sequences
+.SH "SYNOPSIS"
+.HP \w'\fBlistor\fR\ 'u
+\fBlistor\fR \fB\-firstsequences\ \fR\fB\fIseqset\fR\fR \fB\-secondsequences\ \fR\fB\fIseqset\fR\fR [\fB\-operator\ \fR\fB\fIlist\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBlistor\fR\ 'u
+\fBlistor\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBlistor\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-firstsequences\fR \fIseqset\fR
+.RS 4
+.RE
+.PP
+\fB\-secondsequences\fR \fIseqset\fR
+.RS 4
+.RE
+.SS "Additional section"
+.PP
+\fB\-operator\fR \fIlist\fR
+.RS 4
+The following logical operators combine the sequences in the following ways: OR \- gives all that occur in one set or the other AND \- gives only those which occur in both sets XOR \- gives those which only occur in one set or the other, but not in both NOT \- gives those which occur in the first set except for those that also occur in the second Default value: OR
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+The list of sequence names will be written to this list file
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+listor is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/psiphi.1e
+++ emboss-6.4.0/debian/manpages/psiphi.1e
@@ -0,0 +1,87 @@
+'\" t
+.\"     Title: PSIPHI
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "PSIPHI" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+psiphi \- Calculates phi and psi torsion angles from protein coordinates
+.SH "SYNOPSIS"
+.HP \w'\fBpsiphi\fR\ 'u
+\fBpsiphi\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR \fB\-chainnumber\ \fR\fB\fIinteger\fR\fR \fB\-startresiduenumber\ \fR\fB\fIinteger\fR\fR \fB\-finishresiduenumber\ \fR\fB\fIinteger\fR\fR \fB\-outfile\ \fR\fB\fIreport\fR\fR
+.HP \w'\fBpsiphi\fR\ 'u
+\fBpsiphi\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBpsiphi\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "protein:3D structure" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-infile\fR \fIinfile\fR
+.RS 4
+.RE
+.SS "Required section"
+.PP
+\fB\-chainnumber\fR \fIinteger\fR
+.RS 4
+Default value: 1
+.RE
+.PP
+\fB\-startresiduenumber\fR \fIinteger\fR
+.RS 4
+Default value: 1
+.RE
+.PP
+\fB\-finishresiduenumber\fR \fIinteger\fR
+.RS 4
+Default value: 1
+.RE
+.SS "Advanced section"
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIreport\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+psiphi is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/hmoment.1e
+++ emboss-6.4.0/debian/manpages/hmoment.1e
@@ -0,0 +1,106 @@
+'\" t
+.\"     Title: HMOMENT
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "HMOMENT" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+hmoment \- Calculate and plot hydrophobic moment for protein sequence(s)
+.SH "SYNOPSIS"
+.HP \w'\fBhmoment\fR\ 'u
+\fBhmoment\fR \fB\-seqall\ \fR\fB\fIseqall\fR\fR [\fB\-window\ \fR\fB\fIinteger\fR\fR] [\fB\-aangle\ \fR\fB\fIinteger\fR\fR] [\fB\-bangle\ \fR\fB\fIinteger\fR\fR] \fB\-baseline\ \fR\fB\fIfloat\fR\fR \fB\-plot\ \fR\fB\fItoggle\fR\fR \fB\-double\ \fR\fB\fIboolean\fR\fR \fB\-graph\ \fR\fB\fIxygraph\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBhmoment\fR\ 'u
+\fBhmoment\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBhmoment\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Protein:Properties" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-seqall\fR \fIseqall\fR
+.RS 4
+.RE
+.SS "Additional section"
+.PP
+\fB\-window\fR \fIinteger\fR
+.RS 4
+Default value: 10
+.RE
+.PP
+\fB\-aangle\fR \fIinteger\fR
+.RS 4
+Default value: 100
+.RE
+.PP
+\fB\-bangle\fR \fIinteger\fR
+.RS 4
+Default value: 160
+.RE
+.SS "Advanced section"
+.PP
+\fB\-baseline\fR \fIfloat\fR
+.RS 4
+Default value: 0\&.35
+.RE
+.SS "Output section"
+.PP
+\fB\-plot\fR \fItoggle\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-double\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-graph\fR \fIxygraph\fR
+.RS 4
+.RE
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+hmoment is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/featreport.1e
+++ emboss-6.4.0/debian/manpages/featreport.1e
@@ -0,0 +1,74 @@
+'\" t
+.\"     Title: FEATREPORT
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "FEATREPORT" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+featreport \- Reads and writes a feature table
+.SH "SYNOPSIS"
+.HP \w'\fBfeatreport\fR\ 'u
+\fBfeatreport\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR \fB\-features\ \fR\fB\fIfeatures\fR\fR \fB\-outfile\ \fR\fB\fIreport\fR\fR
+.HP \w'\fBfeatreport\fR\ 'u
+\fBfeatreport\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBfeatreport\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIsequence\fR
+.RS 4
+.RE
+.PP
+\fB\-features\fR \fIfeatures\fR
+.RS 4
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIreport\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+featreport is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/garnier.1e
+++ emboss-6.4.0/debian/manpages/garnier.1e
@@ -0,0 +1,76 @@
+'\" t
+.\"     Title: GARNIER
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "GARNIER" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+garnier \- Predicts protein secondary structure using GOR method
+.SH "SYNOPSIS"
+.HP \w'\fBgarnier\fR\ 'u
+\fBgarnier\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-idc\ \fR\fB\fIinteger\fR\fR \fB\-outfile\ \fR\fB\fIreport\fR\fR
+.HP \w'\fBgarnier\fR\ 'u
+\fBgarnier\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBgarnier\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Protein:2D Structure" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqall\fR
+.RS 4
+.RE
+.SS "Advanced section"
+.PP
+\fB\-idc\fR \fIinteger\fR
+.RS 4
+In their paper, GOR mention that if you know something about the secondary structure content of the protein you are analyzing, you can do better in prediction\&. \*(Aqidc\*(Aq is an index into a set of arrays, dharr[] and dsarr[], which provide \*(Aqdecision constants\*(Aq (dch, dcs), which are offsets that are applied to the weights for the helix and sheet (extend) terms\&. So, idc=0 says don\*(Aqt use the decision constant offsets, and idc=1 to 6 indicates that various combinations of dch,dcs offsets should be used\&.
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIreport\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+garnier is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/emowse.1e
+++ emboss-6.4.0/debian/manpages/emowse.1e
@@ -0,0 +1,115 @@
+'\" t
+.\"     Title: EMOWSE
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "EMOWSE" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+emowse \- Search protein sequences by digest fragment molecular weight
+.SH "SYNOPSIS"
+.HP \w'\fBemowse\fR\ 'u
+\fBemowse\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR \fB\-mwdata\ \fR\fB\fIdatafile\fR\fR \fB\-frequencies\ \fR\fB\fIdatafile\fR\fR \fB\-weight\ \fR\fB\fIinteger\fR\fR \fB\-mono\ \fR\fB\fIboolean\fR\fR \fB\-enzyme\ \fR\fB\fIlist\fR\fR \fB\-pcrange\ \fR\fB\fIinteger\fR\fR \fB\-tolerance\ \fR\fB\fIfloat\fR\fR \fB\-partials\ \fR\fB\fIfloat\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBemowse\fR\ 'u
+\fBemowse\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBemowse\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Protein:Composition" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqall\fR
+.RS 4
+.RE
+.PP
+\fB\-infile\fR \fIinfile\fR
+.RS 4
+.RE
+.PP
+\fB\-mwdata\fR \fIdatafile\fR
+.RS 4
+Default value: Emolwt\&.dat
+.RE
+.PP
+\fB\-frequencies\fR \fIdatafile\fR
+.RS 4
+Default value: Efreqs\&.dat
+.RE
+.SS "Required section"
+.PP
+\fB\-weight\fR \fIinteger\fR
+.RS 4
+.RE
+.PP
+\fB\-mono\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.SS "Advanced section"
+.PP
+\fB\-enzyme\fR \fIlist\fR
+.RS 4
+Default value: 1
+.RE
+.PP
+\fB\-pcrange\fR \fIinteger\fR
+.RS 4
+Default value: 25
+.RE
+.PP
+\fB\-tolerance\fR \fIfloat\fR
+.RS 4
+Default value: 0\&.1
+.RE
+.PP
+\fB\-partials\fR \fIfloat\fR
+.RS 4
+Default value: 0\&.4
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+emowse is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/equicktandem.1e
+++ emboss-6.4.0/debian/manpages/equicktandem.1e
@@ -0,0 +1,85 @@
+'\" t
+.\"     Title: EQUICKTANDEM
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "EQUICKTANDEM" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+equicktandem \- Finds tandem repeats in nucleotide sequences
+.SH "SYNOPSIS"
+.HP \w'\fBequicktandem\fR\ 'u
+\fBequicktandem\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR \fB\-maxrepeat\ \fR\fB\fIinteger\fR\fR \fB\-threshold\ \fR\fB\fIinteger\fR\fR \fB\-outfile\ \fR\fB\fIreport\fR\fR \fB\-origfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBequicktandem\fR\ 'u
+\fBequicktandem\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBequicktandem\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Repeats" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIsequence\fR
+.RS 4
+.RE
+.SS "Required section"
+.PP
+\fB\-maxrepeat\fR \fIinteger\fR
+.RS 4
+Default value: 600
+.RE
+.PP
+\fB\-threshold\fR \fIinteger\fR
+.RS 4
+Default value: 20
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIreport\fR
+.RS 4
+.RE
+.PP
+\fB\-origfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+equicktandem is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/dbxuncompress.1e
+++ emboss-6.4.0/debian/manpages/dbxuncompress.1e
@@ -0,0 +1,80 @@
+'\" t
+.\"     Title: DBXUNCOMPRESS
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "DBXUNCOMPRESS" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+dbxuncompress \- Uncompress a compressed dbx index
+.SH "SYNOPSIS"
+.HP \w'\fBdbxuncompress\fR\ 'u
+\fBdbxuncompress\fR \fB\-dbname\ \fR\fB\fIstring\fR\fR \fB\-field\ \fR\fB\fIstring\fR\fR \fB\-indexdir\ \fR\fB\fIdirectory\fR\fR \fB\-$(dbname)\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBdbxuncompress\fR\ 'u
+\fBdbxuncompress\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBdbxuncompress\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Database indexing" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-dbname\fR \fIstring\fR
+.RS 4
+.RE
+.PP
+\fB\-field\fR \fIstring\fR
+.RS 4
+.RE
+.PP
+\fB\-indexdir\fR \fIdirectory\fR
+.RS 4
+.RE
+.SS "Required section"
+.SS "Advanced section"
+.SS "Output section"
+.PP
+\fB\-$(dbname)\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+dbxuncompress is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/texttoxml.1e
+++ emboss-6.4.0/debian/manpages/texttoxml.1e
@@ -0,0 +1,93 @@
+'\" t
+.\"     Title: TEXTTOXML
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "TEXTTOXML" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+texttoxml \- Convert a plain text format to an XML format
+.SH "SYNOPSIS"
+.HP \w'\fBtexttoxml\fR\ 'u
+\fBtexttoxml\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR \fB\-type\ \fR\fB\fIlist\fR\fR \fB\-seq\ \fR\fB\fIlist\fR\fR \fB\-feat\ \fR\fB\fIlist\fR\fR \fB\-align\ \fR\fB\fIlist\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBtexttoxml\fR\ 'u
+\fBtexttoxml\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBtexttoxml\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Misc" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-infile\fR \fIinfile\fR
+.RS 4
+.RE
+.SS "Required section"
+.PP
+\fB\-type\fR \fIlist\fR
+.RS 4
+You must specify the type of file content so that appropriate output format options may be generated\&.
+.RE
+.PP
+\fB\-seq\fR \fIlist\fR
+.RS 4
+This option sets the format of a sequence output file\&. Default value: X
+.RE
+.PP
+\fB\-feat\fR \fIlist\fR
+.RS 4
+This option sets the format of a sequence feature output file\&. Default value: X
+.RE
+.PP
+\fB\-align\fR \fIlist\fR
+.RS 4
+This option sets the format of a sequence alignment output file\&. Default value: X
+.RE
+.SS "Additional section"
+.SS "Advanced section"
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+texttoxml is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/stretcher.1e
+++ emboss-6.4.0/debian/manpages/stretcher.1e
@@ -0,0 +1,90 @@
+'\" t
+.\"     Title: STRETCHER
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "STRETCHER" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+stretcher \- Needleman\-Wunsch rapid global alignment of two sequences
+.SH "SYNOPSIS"
+.HP \w'\fBstretcher\fR\ 'u
+\fBstretcher\fR \fB\-asequence\ \fR\fB\fIsequence\fR\fR \fB\-bsequence\ \fR\fB\fIsequence\fR\fR [\fB\-datafile\ \fR\fB\fImatrix\fR\fR] [\fB\-gapopen\ \fR\fB\fIinteger\fR\fR] [\fB\-gapextend\ \fR\fB\fIinteger\fR\fR] \fB\-outfile\ \fR\fB\fIalign\fR\fR
+.HP \w'\fBstretcher\fR\ 'u
+\fBstretcher\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBstretcher\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Alignment:Global" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-asequence\fR \fIsequence\fR
+.RS 4
+.RE
+.PP
+\fB\-bsequence\fR \fIsequence\fR
+.RS 4
+.RE
+.PP
+\fB\-datafile\fR \fImatrix\fR
+.RS 4
+This is the scoring matrix file used when comparing sequences\&. By default it is the file \*(AqEBLOSUM62\*(Aq (for proteins) or the file \*(AqEDNAFULL\*(Aq (for nucleic sequences)\&. These files are found in the \*(Aqdata\*(Aq directory of the EMBOSS installation\&.
+.RE
+.SS "Additional section"
+.PP
+\fB\-gapopen\fR \fIinteger\fR
+.RS 4
+Default value: @($(acdprotein)? 12 : 16)
+.RE
+.PP
+\fB\-gapextend\fR \fIinteger\fR
+.RS 4
+Default value: @($(acdprotein)? 2 : 4)
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIalign\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+stretcher is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/wordfinder.1e
+++ emboss-6.4.0/debian/manpages/wordfinder.1e
@@ -0,0 +1,122 @@
+'\" t
+.\"     Title: WORDFINDER
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "WORDFINDER" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+wordfinder \- Match large sequences against one or more other sequences
+.SH "SYNOPSIS"
+.HP \w'\fBwordfinder\fR\ 'u
+\fBwordfinder\fR \fB\-asequence\ \fR\fB\fIseqset\fR\fR \fB\-bsequence\ \fR\fB\fIseqall\fR\fR [\fB\-datafile\ \fR\fB\fImatrixf\fR\fR] \fB\-gapopen\ \fR\fB\fIfloat\fR\fR \fB\-gapextend\ \fR\fB\fIfloat\fR\fR [\fB\-width\ \fR\fB\fIinteger\fR\fR] [\fB\-wordlen\ \fR\fB\fIinteger\fR\fR] [\fB\-limitmatch\ \fR\fB\fIinteger\fR\fR] [\fB\-limitalign\ \fR\fB\fIinteger\fR\fR] [\fB\-lowmatch\ \fR\fB\fIinteger\fR\fR] [\fB\-lowalign\ \fR\fB\fIinteger\fR\fR] \fB\-outfile\ \fR\fB\fIalign\fR\fR [\fB\-errorfile\ \fR\fB\fIoutfile\fR\fR]
+.HP \w'\fBwordfinder\fR\ 'u
+\fBwordfinder\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBwordfinder\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Alignment:Local" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-asequence\fR \fIseqset\fR
+.RS 4
+.RE
+.PP
+\fB\-bsequence\fR \fIseqall\fR
+.RS 4
+.RE
+.PP
+\fB\-datafile\fR \fImatrixf\fR
+.RS 4
+This is the scoring matrix file used when comparing sequences\&. By default it is the file \*(AqEBLOSUM62\*(Aq (for proteins) or the file \*(AqEDNAFULL\*(Aq (for nucleic sequences)\&. These files are found in the \*(Aqdata\*(Aq directory of the EMBOSS installation\&.
+.RE
+.SS "Required section"
+.PP
+\fB\-gapopen\fR \fIfloat\fR
+.RS 4
+Default value: @($(acdprotein)? 30\&.0 : 30\&.0)
+.RE
+.PP
+\fB\-gapextend\fR \fIfloat\fR
+.RS 4
+Default value: @($(acdprotein)? 1\&.5 : 1\&.5)
+.RE
+.SS "Additional section"
+.PP
+\fB\-width\fR \fIinteger\fR
+.RS 4
+Default value: 16
+.RE
+.PP
+\fB\-wordlen\fR \fIinteger\fR
+.RS 4
+Default value: 6
+.RE
+.PP
+\fB\-limitmatch\fR \fIinteger\fR
+.RS 4
+.RE
+.PP
+\fB\-limitalign\fR \fIinteger\fR
+.RS 4
+.RE
+.PP
+\fB\-lowmatch\fR \fIinteger\fR
+.RS 4
+.RE
+.PP
+\fB\-lowalign\fR \fIinteger\fR
+.RS 4
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIalign\fR
+.RS 4
+.RE
+.PP
+\fB\-errorfile\fR \fIoutfile\fR
+.RS 4
+Error file to be written to Default value: wordfinder\&.error
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+wordfinder is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/consambig.1e
+++ emboss-6.4.0/debian/manpages/consambig.1e
@@ -0,0 +1,76 @@
+'\" t
+.\"     Title: CONSAMBIG
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "CONSAMBIG" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+consambig \- Create an ambiguous consensus sequence from a multiple alignment
+.SH "SYNOPSIS"
+.HP \w'\fBconsambig\fR\ 'u
+\fBconsambig\fR \fB\-sequence\ \fR\fB\fIseqset\fR\fR \fB\-outseq\ \fR\fB\fIseqout\fR\fR [\fB\-name\ \fR\fB\fIstring\fR\fR]
+.HP \w'\fBconsambig\fR\ 'u
+\fBconsambig\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBconsambig\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Alignment:Consensus" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqset\fR
+.RS 4
+File containing a sequence alignment\&.
+.RE
+.SS "Additional section"
+.SS "Output section"
+.PP
+\fB\-outseq\fR \fIseqout\fR
+.RS 4
+.RE
+.PP
+\fB\-name\fR \fIstring\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+consambig is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/antigenic.1e
+++ emboss-6.4.0/debian/manpages/antigenic.1e
@@ -0,0 +1,76 @@
+'\" t
+.\"     Title: ANTIGENIC
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "ANTIGENIC" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+antigenic \- Finds antigenic sites in proteins
+.SH "SYNOPSIS"
+.HP \w'\fBantigenic\fR\ 'u
+\fBantigenic\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-minlen\ \fR\fB\fIinteger\fR\fR \fB\-outfile\ \fR\fB\fIreport\fR\fR
+.HP \w'\fBantigenic\fR\ 'u
+\fBantigenic\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBantigenic\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Protein:Motifs" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqall\fR
+.RS 4
+.RE
+.SS "Required section"
+.PP
+\fB\-minlen\fR \fIinteger\fR
+.RS 4
+Default value: 6
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIreport\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+antigenic is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/seealso.1e
+++ emboss-6.4.0/debian/manpages/seealso.1e
@@ -0,0 +1,110 @@
+'\" t
+.\"     Title: SEEALSO
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "SEEALSO" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+seealso \- Finds programs with similar function to a specified program
+.SH "SYNOPSIS"
+.HP \w'\fBseealso\fR\ 'u
+\fBseealso\fR \fB\-search\ \fR\fB\fIstring\fR\fR [\fB\-explode\ \fR\fB\fIboolean\fR\fR] \fB\-emboss\ \fR\fB\fIboolean\fR\fR \fB\-embassy\ \fR\fB\fIboolean\fR\fR \fB\-showembassy\ \fR\fB\fIstring\fR\fR [\fB\-outfile\ \fR\fB\fIoutfile\fR\fR] [\fB\-html\ \fR\fB\fItoggle\fR\fR] [\fB\-groups\ \fR\fB\fIboolean\fR\fR] \fB\-colon\ \fR\fB\fIboolean\fR\fR
+.HP \w'\fBseealso\fR\ 'u
+\fBseealso\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBseealso\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Documentation" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-search\fR \fIstring\fR
+.RS 4
+Enter the name of an EMBOSS program
+.RE
+.SS "Additional section"
+.PP
+\fB\-explode\fR \fIboolean\fR
+.RS 4
+The groups that EMBOSS applications belong to have two forms, exploded and not exploded\&. The exploded group names are more numerous and often vaguely phrased than the non\-exploded ones\&. The exploded names are formed from definitions of the group names that start like NAME1:NAME2 and which are then expanded into many combinations of the names as: \*(AqNAME1\*(Aq, \*(AqNAME2\*(Aq, \*(AqNAME1 NAME2\*(Aq, NAME2 NAME1\*(Aq\&. The non\-expanded names are simply like: \*(AqNAME1 NAME2\*(Aq\&. Using expanded group names will find many more programs which share at least some of the expanded names than using the non\-exploded names and so you will get more programs reported as sharing a similar function than you will if you specify that you wish to use non\-exploded names Default value: N
+.RE
+.SS "Advanced section"
+.PP
+\fB\-emboss\fR \fIboolean\fR
+.RS 4
+If you use this option then EMBOSS program documentation will be searched\&. If this option is set to be false, then only the EMBASSY programs will be searched (if the \-embassy option is true)\&. EMBASSY programs are not strictly part of EMBOSS, but use the same code libraries and share the same look and feel, but are generally developed by people who wish the programs to be outside of the GNU Public Licence scheme Default value: Y
+.RE
+.PP
+\fB\-embassy\fR \fIboolean\fR
+.RS 4
+If you use this option then EMBASSY program documentation will be searched\&. If this option is set to be false, then only the EMBOSS programs will be searched (if the \-emboss option is true)\&. EMBASSY programs are not strictly part of EMBOSS, but use the same code libraries and share the same look and feel, but are generally developed by people who wish the programs to be outside of the GNU Public Licence scheme Default value: Y
+.RE
+.PP
+\fB\-showembassy\fR \fIstring\fR
+.RS 4
+If you use this option then this EMBASSY package program documentation will be searched\&. EMBASSY programs are not strictly part of EMBOSS, but use the same code libraries and share the same look and feel, but are generally developed by people who wish the programs to be outside of the GNU Public Licence scheme
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+Default value: stdout
+.RE
+.SS "Html section"
+.PP
+\fB\-html\fR \fItoggle\fR
+.RS 4
+If you are sending the output to a file, this will format it for displaying as a table in a WWW document\&. Default value: N
+.RE
+.PP
+\fB\-groups\fR \fIboolean\fR
+.RS 4
+If you use this option, then only the group names will output to the file Default value: N
+.RE
+.PP
+\fB\-colon\fR \fIboolean\fR
+.RS 4
+The groups that EMBOSS applications belong to have up to two levels, for example the primary group \*(AqALIGNMENT\*(Aq has several sub\-groups, or second\-level groups, e\&.g\&.: CONSENSUS, DIFFERENCES, DOT PLOTS, GLOBAL, LOCAL, MULTIPLE\&. To aid programs that parse the output of seealso that require the names of these subgroups, a colon \*(Aq:\*(Aq will be placed between the first and second level of the group name if this option is true\&. Default value: N
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+seealso is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/acdpretty.1e
+++ emboss-6.4.0/debian/manpages/acdpretty.1e
@@ -0,0 +1,60 @@
+'\" t
+.\"     Title: ACDPRETTY
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "ACDPRETTY" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+acdpretty \- Correctly reformat an application ACD file
+.SH "SYNOPSIS"
+.HP \w'\fBacdpretty\fR\ 'u
+\fBacdpretty\fR
+.HP \w'\fBacdpretty\fR\ 'u
+\fBacdpretty\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBacdpretty\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Acd,Data retrieval:Tool data" command group(s)\&.
+.SH "OPTIONS"
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+acdpretty is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/prosextract.1e
+++ emboss-6.4.0/debian/manpages/prosextract.1e
@@ -0,0 +1,65 @@
+'\" t
+.\"     Title: PROSEXTRACT
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "PROSEXTRACT" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+prosextract \- Processes the PROSITE motif database for use by patmatmotifs
+.SH "SYNOPSIS"
+.HP \w'\fBprosextract\fR\ 'u
+\fBprosextract\fR \fB\-prositedir\ \fR\fB\fIdirectory\fR\fR
+.HP \w'\fBprosextract\fR\ 'u
+\fBprosextract\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBprosextract\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Database creation" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-prositedir\fR \fIdirectory\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+prosextract is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/showorf.1e
+++ emboss-6.4.0/debian/manpages/showorf.1e
@@ -0,0 +1,101 @@
+'\" t
+.\"     Title: SHOWORF
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "SHOWORF" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+showorf \- Display a nucleotide sequence and translation in pretty format
+.SH "SYNOPSIS"
+.HP \w'\fBshoworf\fR\ 'u
+\fBshoworf\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR \fB\-frames\ \fR\fB\fIlist\fR\fR [\fB\-table\ \fR\fB\fIlist\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-ruler\ \fR\fB\fIboolean\fR\fR] [\fB\-plabel\ \fR\fB\fIboolean\fR\fR] [\fB\-nlabel\ \fR\fB\fIboolean\fR\fR] \fB\-width\ \fR\fB\fIinteger\fR\fR
+.HP \w'\fBshoworf\fR\ 'u
+\fBshoworf\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBshoworf\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Gene finding,Nucleic:Translation" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIsequence\fR
+.RS 4
+.RE
+.SS "Required section"
+.PP
+\fB\-frames\fR \fIlist\fR
+.RS 4
+Default value: 1,2,3,4,5,6
+.RE
+.SS "Additional section"
+.PP
+\fB\-table\fR \fIlist\fR
+.RS 4
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.PP
+\fB\-ruler\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-plabel\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-nlabel\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-width\fR \fIinteger\fR
+.RS 4
+Default value: 50
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+showorf is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/maskfeat.1e
+++ emboss-6.4.0/debian/manpages/maskfeat.1e
@@ -0,0 +1,86 @@
+'\" t
+.\"     Title: MASKFEAT
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "MASKFEAT" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+maskfeat \- Write a sequence with masked features
+.SH "SYNOPSIS"
+.HP \w'\fBmaskfeat\fR\ 'u
+\fBmaskfeat\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR [\fB\-type\ \fR\fB\fIstring\fR\fR] [\fB\-tolower\ \fR\fB\fItoggle\fR\fR] \fB\-maskchar\ \fR\fB\fIstring\fR\fR \fB\-outseq\ \fR\fB\fIseqout\fR\fR
+.HP \w'\fBmaskfeat\fR\ 'u
+\fBmaskfeat\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBmaskfeat\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit,Feature tables" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqall\fR
+.RS 4
+.RE
+.SS "Additional section"
+.PP
+\fB\-type\fR \fIstring\fR
+.RS 4
+By default any feature in the feature table with a type starting \*(Aqrepeat\*(Aq is masked\&. You can set this to be any feature type you wish to mask\&. See http://www\&.ebi\&.ac\&.uk/embl/WebFeat/ for a list of the EMBL feature types and see Appendix A of the Swissprot user manual in http://www\&.expasy\&.org/sprot/userman\&.html for a list of the Swissprot feature types\&. The type may be wildcarded by using \*(Aq*\*(Aq\&. If you wish to mask more than one type, separate their names with spaces or commas, eg: *UTR repeat* Default value: repeat*
+.RE
+.PP
+\fB\-tolower\fR \fItoggle\fR
+.RS 4
+The region can be \*(Aqmasked\*(Aq by converting the sequence characters to lower\-case, some non\-EMBOSS programs e\&.g\&. fasta can interpret this as a masked region\&. The sequence is unchanged apart from the case change\&. You might like to ensure that the whole sequence is in upper\-case before masking the specified regions to lower\-case by using the \*(Aq\-supper\*(Aq flag\&. Default value: N
+.RE
+.PP
+\fB\-maskchar\fR \fIstring\fR
+.RS 4
+Character to use when masking\&. Default is \*(AqX\*(Aq for protein sequences, \*(AqN\*(Aq for nucleic sequences\&. If the mask character is set to be the SPACE character or a null character, then the sequence is \*(Aqmasked\*(Aq by changing it to lower\-case, just as with the \*(Aq\-lowercase\*(Aq flag\&. Default value: @($(acdprotein)?X:N)
+.RE
+.SS "Output section"
+.PP
+\fB\-outseq\fR \fIseqout\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+maskfeat is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/histogramtest.1e
+++ emboss-6.4.0/debian/manpages/histogramtest.1e
@@ -0,0 +1,90 @@
+'\" t
+.\"     Title: HISTOGRAMTEST
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "HISTOGRAMTEST" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+histogramtest \- Test of graphics
+.SH "SYNOPSIS"
+.HP \w'\fBhistogramtest\fR\ 'u
+\fBhistogramtest\fR \fB\-sets\ \fR\fB\fIinteger\fR\fR \fB\-points\ \fR\fB\fIinteger\fR\fR \fB\-bins\ \fR\fB\fIinteger\fR\fR \fB\-xstart\ \fR\fB\fIinteger\fR\fR \fB\-xend\ \fR\fB\fIinteger\fR\fR \fB\-graph\ \fR\fB\fIxygraph\fR\fR
+.HP \w'\fBhistogramtest\fR\ 'u
+\fBhistogramtest\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBhistogramtest\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Test" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sets\fR \fIinteger\fR
+.RS 4
+Default value: 1
+.RE
+.PP
+\fB\-points\fR \fIinteger\fR
+.RS 4
+Default value: 10
+.RE
+.PP
+\fB\-bins\fR \fIinteger\fR
+.RS 4
+Default value: $(points)
+.RE
+.PP
+\fB\-xstart\fR \fIinteger\fR
+.RS 4
+.RE
+.PP
+\fB\-xend\fR \fIinteger\fR
+.RS 4
+Default value: @($(xstart)+$(points))
+.RE
+.SS "Output section"
+.PP
+\fB\-graph\fR \fIxygraph\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+histogramtest is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/prettyseq.1e
+++ emboss-6.4.0/debian/manpages/prettyseq.1e
@@ -0,0 +1,102 @@
+'\" t
+.\"     Title: PRETTYSEQ
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "PRETTYSEQ" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+prettyseq \- Write a nucleotide sequence and its translation to file
+.SH "SYNOPSIS"
+.HP \w'\fBprettyseq\fR\ 'u
+\fBprettyseq\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR \fB\-range\ \fR\fB\fIrange\fR\fR [\fB\-table\ \fR\fB\fIlist\fR\fR] [\fB\-ruler\ \fR\fB\fIboolean\fR\fR] [\fB\-plabel\ \fR\fB\fIboolean\fR\fR] [\fB\-nlabel\ \fR\fB\fIboolean\fR\fR] \fB\-width\ \fR\fB\fIinteger\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBprettyseq\fR\ 'u
+\fBprettyseq\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBprettyseq\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Translation,Display" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIsequence\fR
+.RS 4
+.RE
+.SS "Required section"
+.PP
+\fB\-range\fR \fIrange\fR
+.RS 4
+Default value: $(sequence\&.begin)\-$(sequence\&.end)
+.RE
+.SS "Additional section"
+.PP
+\fB\-table\fR \fIlist\fR
+.RS 4
+.RE
+.PP
+\fB\-ruler\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-plabel\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-nlabel\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.SS "Advanced section"
+.PP
+\fB\-width\fR \fIinteger\fR
+.RS 4
+Default value: 60
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+prettyseq is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/entrailswiki.1e
+++ emboss-6.4.0/debian/manpages/entrailswiki.1e
@@ -0,0 +1,71 @@
+'\" t
+.\"     Title: ENTRAILSWIKI
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "ENTRAILSWIKI" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+entrailswiki \- Reports the internal structures in wikitext
+.SH "SYNOPSIS"
+.HP \w'\fBentrailswiki\fR\ 'u
+\fBentrailswiki\fR \fB\-tables\ \fR\fB\fIlist\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBentrailswiki\fR\ 'u
+\fBentrailswiki\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBentrailswiki\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Misc" command group(s)\&.
+.SH "OPTIONS"
+.SS "required section"
+.PP
+\fB\-tables\fR \fIlist\fR
+.RS 4
+Default value: all
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+entrailswiki is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/lindna.1e
+++ emboss-6.4.0/debian/manpages/lindna.1e
@@ -0,0 +1,157 @@
+'\" t
+.\"     Title: LINDNA
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "LINDNA" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+lindna \- Draws linear maps of DNA constructs
+.SH "SYNOPSIS"
+.HP \w'\fBlindna\fR\ 'u
+\fBlindna\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR [\fB\-maxgroups\ \fR\fB\fIinteger\fR\fR] [\fB\-maxlabels\ \fR\fB\fIinteger\fR\fR] \fB\-ruler\ \fR\fB\fIboolean\fR\fR \fB\-blocktype\ \fR\fB\fIlist\fR\fR [\fB\-intersymbol\ \fR\fB\fIselection\fR\fR] [\fB\-intercolour\ \fR\fB\fIinteger\fR\fR] [\fB\-interticks\ \fR\fB\fIboolean\fR\fR] [\fB\-gapsize\ \fR\fB\fIinteger\fR\fR] [\fB\-ticklines\ \fR\fB\fIboolean\fR\fR] [\fB\-textheight\ \fR\fB\fIfloat\fR\fR] [\fB\-textlength\ \fR\fB\fIfloat\fR\fR] [\fB\-margin\ \fR\fB\fIfloat\fR\fR] [\fB\-tickheight\ \fR\fB\fIfloat\fR\fR] [\fB\-blockheight\ \fR\fB\fIfloat\fR\fR] [\fB\-rangeheight\ \fR\fB\fIfloat\fR\fR] [\fB\-gapgroup\ \fR\fB\fIfloat\fR\fR] [\fB\-postext\ \fR\fB\fIfloat\fR\fR] \fB\-graphout\ \fR\fB\fIgraph\fR\fR
+.HP \w'\fBlindna\fR\ 'u
+\fBlindna\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBlindna\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Display" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-infile\fR \fIinfile\fR
+.RS 4
+Default value: inputfile
+.RE
+.SS "Additional section"
+.PP
+\fB\-maxgroups\fR \fIinteger\fR
+.RS 4
+Default value: 20
+.RE
+.PP
+\fB\-maxlabels\fR \fIinteger\fR
+.RS 4
+Default value: 10000
+.RE
+.SS "Output section"
+.PP
+\fB\-ruler\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-blocktype\fR \fIlist\fR
+.RS 4
+Default value: Filled
+.RE
+.PP
+\fB\-intersymbol\fR \fIselection\fR
+.RS 4
+Default value: Straight
+.RE
+.PP
+\fB\-intercolour\fR \fIinteger\fR
+.RS 4
+Default value: 1
+.RE
+.PP
+\fB\-interticks\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-gapsize\fR \fIinteger\fR
+.RS 4
+A zero value allows the application to choose a gap size
+.RE
+.PP
+\fB\-ticklines\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-textheight\fR \fIfloat\fR
+.RS 4
+Height of text\&. Enter a number <1\&.0 or >1\&.0 to decrease or increase the size, respectively Default value: 1\&.0
+.RE
+.PP
+\fB\-textlength\fR \fIfloat\fR
+.RS 4
+Length of text\&. Enter a number <1\&.0 or >1\&.0 to decrease or increase the size, respectively Default value: 1\&.0
+.RE
+.PP
+\fB\-margin\fR \fIfloat\fR
+.RS 4
+Width of left margin\&. This is the region left to the groups where the names of the groups are displayed\&. Enter a number <1\&.0 or >1\&.0 to decrease or increase the size, respectively Default value: 1\&.0
+.RE
+.PP
+\fB\-tickheight\fR \fIfloat\fR
+.RS 4
+Height of ticks\&. Enter a number <1\&.0 or >1\&.0 to decrease or increase the size, respectively Default value: 1\&.0
+.RE
+.PP
+\fB\-blockheight\fR \fIfloat\fR
+.RS 4
+Height of blocks\&. Enter a number <1\&.0 or >1\&.0 to decrease or increase the size, respectively Default value: 1
+.RE
+.PP
+\fB\-rangeheight\fR \fIfloat\fR
+.RS 4
+Height of range ends\&. Enter a number <1\&.0 or >1\&.0 to decrease or increase the size, respectively Default value: 1\&.0
+.RE
+.PP
+\fB\-gapgroup\fR \fIfloat\fR
+.RS 4
+Space between groups\&. Enter a number <1\&.0 or >1\&.0 to decrease or increase the size, respectively Default value: 1\&.0
+.RE
+.PP
+\fB\-postext\fR \fIfloat\fR
+.RS 4
+Space between text and ticks, blocks, and ranges\&. Enter a number <1\&.0 or >1\&.0 to decrease or increase the size, respectively Default value: 1\&.0
+.RE
+.PP
+\fB\-graphout\fR \fIgraph\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+lindna is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/textsearch.1e
+++ emboss-6.4.0/debian/manpages/textsearch.1e
@@ -0,0 +1,117 @@
+'\" t
+.\"     Title: TEXTSEARCH
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "TEXTSEARCH" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+textsearch \- Search the textual description of sequence(s)
+.SH "SYNOPSIS"
+.HP \w'\fBtextsearch\fR\ 'u
+\fBtextsearch\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-pattern\ \fR\fB\fIstring\fR\fR [\fB\-casesensitive\ \fR\fB\fIboolean\fR\fR] [\fB\-html\ \fR\fB\fIboolean\fR\fR] \fB\-only\ \fR\fB\fIboolean\fR\fR \fB\-heading\ \fR\fB\fIboolean\fR\fR \fB\-usa\ \fR\fB\fIboolean\fR\fR \fB\-accession\ \fR\fB\fIboolean\fR\fR \fB\-name\ \fR\fB\fIboolean\fR\fR \fB\-description\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBtextsearch\fR\ 'u
+\fBtextsearch\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBtextsearch\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Data retrieval:Text data" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqall\fR
+.RS 4
+.RE
+.SS "Required section"
+.PP
+\fB\-pattern\fR \fIstring\fR
+.RS 4
+The search pattern is a regular expression\&. Use a | to indicate OR\&. For example: human|mouse will find text with either \*(Aqhuman\*(Aq OR \*(Aqmouse\*(Aq in the text
+.RE
+.SS "Additional section"
+.PP
+\fB\-casesensitive\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.SS "Output section"
+.PP
+\fB\-html\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-only\fR \fIboolean\fR
+.RS 4
+This is a way of shortening the command line if you only want a few things to be displayed\&. Instead of specifying: \*(Aq\-nohead \-noname \-nousa \-noacc \-nodesc\*(Aq to get only the name output, you can specify \*(Aq\-only \-name\*(Aq Default value: N
+.RE
+.PP
+\fB\-heading\fR \fIboolean\fR
+.RS 4
+Default value: @(!$(only))
+.RE
+.PP
+\fB\-usa\fR \fIboolean\fR
+.RS 4
+Default value: @(!$(only))
+.RE
+.PP
+\fB\-accession\fR \fIboolean\fR
+.RS 4
+Default value: @(!$(only))
+.RE
+.PP
+\fB\-name\fR \fIboolean\fR
+.RS 4
+Default value: @(!$(only))
+.RE
+.PP
+\fB\-description\fR \fIboolean\fR
+.RS 4
+Default value: @(!$(only))
+.RE
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+textsearch is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/aligncopypair.1e
+++ emboss-6.4.0/debian/manpages/aligncopypair.1e
@@ -0,0 +1,87 @@
+'\" t
+.\"     Title: ALIGNCOPYPAIR
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "ALIGNCOPYPAIR" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+aligncopypair \- Reads and writes pairs from alignments
+.SH "SYNOPSIS"
+.HP \w'\fBaligncopypair\fR\ 'u
+\fBaligncopypair\fR \fB\-sequences\ \fR\fB\fIseqset\fR\fR [\fB\-name\ \fR\fB\fIstring\fR\fR] [\fB\-comment\ \fR\fB\fIstring\fR\fR] [\fB\-append\ \fR\fB\fIboolean\fR\fR] \fB\-outfile\ \fR\fB\fIalign\fR\fR
+.HP \w'\fBaligncopypair\fR\ 'u
+\fBaligncopypair\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBaligncopypair\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequences\fR \fIseqset\fR
+.RS 4
+File containing a sequence alignment\&.
+.RE
+.SS "Required section"
+.SS "Additional section"
+.PP
+\fB\-name\fR \fIstring\fR
+.RS 4
+.RE
+.PP
+\fB\-comment\fR \fIstring\fR
+.RS 4
+.RE
+.PP
+\fB\-append\fR \fIboolean\fR
+.RS 4
+This allows you to append the name and comments you have given on to the end of the existing alignment header\&. Default value: N
+.RE
+.SS "Advanced section"
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIalign\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+aligncopypair is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/goseq.1e
+++ emboss-6.4.0/debian/manpages/goseq.1e
@@ -0,0 +1,79 @@
+'\" t
+.\"     Title: GOSEQ
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "GOSEQ" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+goseq \- Identify sequence entries containing GO terms
+.SH "SYNOPSIS"
+.HP \w'\fBgoseq\fR\ 'u
+\fBgoseq\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-term\ \fR\fB\fIstring\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBgoseq\fR\ 'u
+\fBgoseq\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBgoseq\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqall\fR
+.RS 4
+.RE
+.PP
+\fB\-term\fR \fIstring\fR
+.RS 4
+This is the name of a term from the GO ontology\&. If you are not sure what names are available, use ontoget\&.
+.RE
+.SS "Required section"
+.SS "Additional section"
+.SS "Advanced section"
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+The list of sequence names will be written to this list file
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+goseq is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/taxseq.1e
+++ emboss-6.4.0/debian/manpages/taxseq.1e
@@ -0,0 +1,78 @@
+'\" t
+.\"     Title: TAXSEQ
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "TAXSEQ" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+taxseq \- Identify sequence entries containing taxonomy IDs
+.SH "SYNOPSIS"
+.HP \w'\fBtaxseq\fR\ 'u
+\fBtaxseq\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-ids\ \fR\fB\fIstring\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBtaxseq\fR\ 'u
+\fBtaxseq\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBtaxseq\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqall\fR
+.RS 4
+.RE
+.PP
+\fB\-ids\fR \fIstring\fR
+.RS 4
+.RE
+.SS "Required section"
+.SS "Additional section"
+.SS "Advanced section"
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+The list of sequence names will be written to this list file
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+taxseq is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/polydot.1e
+++ emboss-6.4.0/debian/manpages/polydot.1e
@@ -0,0 +1,96 @@
+'\" t
+.\"     Title: POLYDOT
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "POLYDOT" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+polydot \- Draw dotplots for all\-against\-all comparison of a sequence set
+.SH "SYNOPSIS"
+.HP \w'\fBpolydot\fR\ 'u
+\fBpolydot\fR \fB\-sequences\ \fR\fB\fIseqset\fR\fR \fB\-wordsize\ \fR\fB\fIinteger\fR\fR \fB\-gap\ \fR\fB\fIinteger\fR\fR [\fB\-boxit\ \fR\fB\fIboolean\fR\fR] [\fB\-dumpfeat\ \fR\fB\fItoggle\fR\fR] \fB\-outfeat\ \fR\fB\fIfeatout\fR\fR \fB\-graph\ \fR\fB\fIgraph\fR\fR
+.HP \w'\fBpolydot\fR\ 'u
+\fBpolydot\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBpolydot\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Alignment:Dot plots" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequences\fR \fIseqset\fR
+.RS 4
+File containing a sequence alignment
+.RE
+.SS "Required section"
+.PP
+\fB\-wordsize\fR \fIinteger\fR
+.RS 4
+Default value: 6
+.RE
+.SS "Output section"
+.PP
+\fB\-gap\fR \fIinteger\fR
+.RS 4
+This specifies the size of the gap that is used to separate the individual dotplots in the display\&. The size is measured in residues, as displayed in the output\&. Default value: 10
+.RE
+.PP
+\fB\-boxit\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-dumpfeat\fR \fItoggle\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-outfeat\fR \fIfeatout\fR
+.RS 4
+.RE
+.PP
+\fB\-graph\fR \fIgraph\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+polydot is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/martregistry.1e
+++ emboss-6.4.0/debian/manpages/martregistry.1e
@@ -0,0 +1,81 @@
+'\" t
+.\"     Title: MARTREGISTRY
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "MARTREGISTRY" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+martregistry \- Show Biomart registries listed on a host
+.SH "SYNOPSIS"
+.HP \w'\fBmartregistry\fR\ 'u
+\fBmartregistry\fR \fB\-host\ \fR\fB\fIstring\fR\fR \fB\-path\ \fR\fB\fIstring\fR\fR \fB\-port\ \fR\fB\fIinteger\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBmartregistry\fR\ 'u
+\fBmartregistry\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBmartregistry\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-host\fR \fIstring\fR
+.RS 4
+Default value: www\&.biomart\&.org
+.RE
+.PP
+\fB\-path\fR \fIstring\fR
+.RS 4
+Default value: /biomart/martservice
+.RE
+.PP
+\fB\-port\fR \fIinteger\fR
+.RS 4
+Default value: 80
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+martregistry is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/charge.1e
+++ emboss-6.4.0/debian/manpages/charge.1e
@@ -0,0 +1,90 @@
+'\" t
+.\"     Title: CHARGE
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "CHARGE" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+charge \- Draw a protein charge plot
+.SH "SYNOPSIS"
+.HP \w'\fBcharge\fR\ 'u
+\fBcharge\fR \fB\-seqall\ \fR\fB\fIseqall\fR\fR \fB\-aadata\ \fR\fB\fIdatafile\fR\fR [\fB\-window\ \fR\fB\fIinteger\fR\fR] \fB\-plot\ \fR\fB\fItoggle\fR\fR \fB\-graph\ \fR\fB\fIxygraph\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBcharge\fR\ 'u
+\fBcharge\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBcharge\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Protein:Properties" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-seqall\fR \fIseqall\fR
+.RS 4
+.RE
+.PP
+\fB\-aadata\fR \fIdatafile\fR
+.RS 4
+Default value: Eamino\&.dat
+.RE
+.SS "Additional section"
+.PP
+\fB\-window\fR \fIinteger\fR
+.RS 4
+Default value: 5
+.RE
+.SS "Output section"
+.PP
+\fB\-plot\fR \fItoggle\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-graph\fR \fIxygraph\fR
+.RS 4
+.RE
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+charge is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/seqcount.1e
+++ emboss-6.4.0/debian/manpages/seqcount.1e
@@ -0,0 +1,70 @@
+'\" t
+.\"     Title: SEQCOUNT
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "SEQCOUNT" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+seqcount \- Reads and counts sequences
+.SH "SYNOPSIS"
+.HP \w'\fBseqcount\fR\ 'u
+\fBseqcount\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBseqcount\fR\ 'u
+\fBseqcount\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBseqcount\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqall\fR
+.RS 4
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+seqcount is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/isdbname.1e
+++ emboss-6.4.0/debian/manpages/isdbname.1e
@@ -0,0 +1,79 @@
+'\" t
+.\"     Title: ISDBNAME
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "ISDBNAME" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+isdbname \- Check whether a supplied string is a known database name
+.SH "SYNOPSIS"
+.HP \w'\fBisdbname\fR\ 'u
+\fBisdbname\fR [\fB\-term\ \fR\fB\fIstring\fR\fR] [\fB\-infout\ \fR\fB\fItoggle\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBisdbname\fR\ 'u
+\fBisdbname\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBisdbname\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Information" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-term\fR \fIstring\fR
+.RS 4
+.RE
+.SS "Required section"
+.SS "Additional section"
+.PP
+\fB\-infout\fR \fItoggle\fR
+.RS 4
+This option will write to file information (from the EMBOSS data file DRCAT\&.dat) for the database with a name that matches the supplied string\&. Default value: N
+.RE
+.SS "Advanced section"
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+Default value: stdout
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+isdbname is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/checktrans.1e
+++ emboss-6.4.0/debian/manpages/checktrans.1e
@@ -0,0 +1,92 @@
+'\" t
+.\"     Title: CHECKTRANS
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "CHECKTRANS" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+checktrans \- Reports STOP codons and ORF statistics of a protein
+.SH "SYNOPSIS"
+.HP \w'\fBchecktrans\fR\ 'u
+\fBchecktrans\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-orfml\ \fR\fB\fIinteger\fR\fR [\fB\-addlast\ \fR\fB\fIboolean\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR \fB\-outfeat\ \fR\fB\fIfeatout\fR\fR
+.HP \w'\fBchecktrans\fR\ 'u
+\fBchecktrans\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBchecktrans\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Gene finding,Nucleic:Translation" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqall\fR
+.RS 4
+.RE
+.SS "Required section"
+.PP
+\fB\-orfml\fR \fIinteger\fR
+.RS 4
+Default value: 100
+.RE
+.SS "Additional section"
+.PP
+\fB\-addlast\fR \fIboolean\fR
+.RS 4
+An asterisk in the protein sequence indicates the position of a STOP codon\&. Checktrans assumes that all ORFs end in a STOP codon\&. Forcing the sequence to end with an asterisk, if there is not one there already, makes checktrans treat the end as a potential ORF\&. If an asterisk is added, it is not included in the reported count of STOPs\&. Default value: Y
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.PP
+\fB\-outseq\fR \fIseqoutall\fR
+.RS 4
+Sequence file to hold output ORF sequences
+.RE
+.PP
+\fB\-outfeat\fR \fIfeatout\fR
+.RS 4
+File for output features
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+checktrans is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/eprimer32.1e
+++ emboss-6.4.0/debian/manpages/eprimer32.1e
@@ -0,0 +1,375 @@
+'\" t
+.\"     Title: EPRIMER32
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "EPRIMER32" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+eprimer32 \- Picks PCR primers and hybridization oligos
+.SH "SYNOPSIS"
+.HP \w'\fBeprimer32\fR\ 'u
+\fBeprimer32\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR [\fB\-primer\ \fR\fB\fItoggle\fR\fR] \fB\-task\ \fR\fB\fIlist\fR\fR [\fB\-hybridprobe\ \fR\fB\fItoggle\fR\fR] \fB\-mishyblibraryfile\ \fR\fB\fIinfile\fR\fR \fB\-mispriminglibraryfile\ \fR\fB\fIinfile\fR\fR [\fB\-numreturn\ \fR\fB\fIinteger\fR\fR] [\fB\-includedregion\ \fR\fB\fIrange\fR\fR] [\fB\-targetregion\ \fR\fB\fIrange\fR\fR] [\fB\-excludedregion\ \fR\fB\fIrange\fR\fR] [\fB\-forwardinput\ \fR\fB\fIstring\fR\fR] [\fB\-reverseinput\ \fR\fB\fIstring\fR\fR] \fB\-gcclamp\ \fR\fB\fIinteger\fR\fR \fB\-osize\ \fR\fB\fIinteger\fR\fR \fB\-minsize\ \fR\fB\fIinteger\fR\fR \fB\-maxsize\ \fR\fB\fIinteger\fR\fR \fB\-otm\ \fR\fB\fIfloat\fR\fR \fB\-mintm\ \fR\fB\fIfloat\fR\fR \fB\-maxtm\ \fR\fB\fIfloat\fR\fR \fB\-maxdifftm\ \fR\fB\fIfloat\fR\fR \fB\-ogcpercent\ \fR\fB\fIfloat\fR\fR \fB\-mingc\ \fR\fB\fIfloat\fR\fR \fB\-maxgc\ \fR\fB\fIfloat\fR\fR \fB\-saltconc\ \fR\fB\fIfloat\fR\fR \fB\-dnaconc\ \fR\fB\fIfloat\fR\fR \fB\-maxpolyx\ \fR\fB\fIinteger\fR\fR \fB\-psizeopt\ \fR\fB\fIinteger\fR\fR \fB\-prange\ \fR\fB\fIrange\fR\fR \fB\-ptmopt\ \fR\fB\fIfloat\fR\fR \fB\-ptmmin\ \fR\fB\fIfloat\fR\fR \fB\-ptmmax\ \fR\fB\fIfloat\fR\fR \fB\-oexcludedregion\ \fR\fB\fIrange\fR\fR \fB\-oligoinput\ \fR\fB\fIstring\fR\fR \fB\-osizeopt\ \fR\fB\fIinteger\fR\fR \fB\-ominsize\ \fR\fB\fIinteger\fR\fR \fB\-omaxsize\ \fR\fB\fIinteger\fR\fR \fB\-otmopt\ \fR\fB\fIfloat\fR\fR \fB\-otmmin\ \fR\fB\fIfloat\fR\fR \fB\-otmmax\ \fR\fB\fIfloat\fR\fR \fB\-ogcopt\ \fR\fB\fIfloat\fR\fR \fB\-ogcmin\ \fR\fB\fIfloat\fR\fR \fB\-ogcmax\ \fR\fB\fIfloat\fR\fR \fB\-osaltconc\ \fR\fB\fIfloat\fR\fR \fB\-odnaconc\ \fR\fB\fIfloat\fR\fR \fB\-oanyself\ \fR\fB\fIfloat\fR\fR \fB\-oendself\ \fR\fB\fIfloat\fR\fR \fB\-opolyxmax\ \fR\fB\fIinteger\fR\fR \fB\-omishybmax\ \fR\fB\fIfloat\fR\fR \fB\-explainflag\ \fR\fB\fIboolean\fR\fR \fB\-fileflag\ \fR\fB\fIboolean\fR\fR \fB\-firstbaseindex\ \fR\fB\fIinteger\fR\fR \fB\-pickanyway\ \fR\fB\fIboolean\fR\fR \fB\-maxmispriming\ \fR\fB\fIfloat\fR\fR \fB\-pairmaxmispriming\ \fR\fB\fIfloat\fR\fR \fB\-numnsaccepted\ \fR\fB\fIinteger\fR\fR \fB\-selfany\ \fR\fB\fIfloat\fR\fR \fB\-selfend\ \fR\fB\fIfloat\fR\fR \fB\-scorrection\ \fR\fB\fIlist\fR\fR \fB\-tmformula\ \fR\fB\fIlist\fR\fR \fB\-maxendstability\ \fR\fB\fIfloat\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBeprimer32\fR\ 'u
+\fBeprimer32\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBeprimer32\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Primers" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqall\fR
+.RS 4
+The sequence from which to choose primers\&. The sequence must be presented 5\*(Aq to 3\*(Aq
+.RE
+.PP
+\fB\-primer\fR \fItoggle\fR
+.RS 4
+Tell Eprimer32 to pick primer(s) Default value: Y
+.RE
+.PP
+\fB\-task\fR \fIlist\fR
+.RS 4
+Tell Eprimer32 what task to perform\&. Legal values are 1: \*(AqPick PCR primers\*(Aq, 2: \*(AqPick forward primer only\*(Aq, 3: \*(AqPick reverse primer only\*(Aq, 4: \*(AqNo primers needed\*(Aq\&. Default value: 1
+.RE
+.PP
+\fB\-hybridprobe\fR \fItoggle\fR
+.RS 4
+An \*(Aqinternal oligo\*(Aq is intended to be used as a hybridization probe (hyb probe) to detect the PCR product after amplification\&. Default value: N
+.RE
+.PP
+\fB\-mishyblibraryfile\fR \fIinfile\fR
+.RS 4
+Similar to MISPRIMING\-LIBRARY, except that the event we seek to avoid is hybridization of the internal oligo to sequences in this library rather than priming from them\&. The file must be in (a slightly restricted) FASTA format (W\&. B\&. Pearson and D\&.J\&. Lipman, PNAS 85:8 pp 2444\-2448 [1988]); we briefly discuss the organization of this file below\&. If this parameter is specified then Eprimer32 locally aligns each candidate oligo against each library sequence and rejects those primers for which the local alignment score times a specified weight (see below) exceeds INTERNAL\-OLIGO\-MAX\-MISHYB\&. (The maximum value of the weight is arbitrarily set to 12\&.0\&.) Each sequence entry in the FASTA\-format file must begin with an \*(Aqid line\*(Aq that starts with \*(Aq>\*(Aq\&. The contents of the id line is \*(Aqslightly restricted\*(Aq in that Eprimer32 parses everything after any optional asterisk (\*(Aq*\*(Aq) as a floating point number to use as the weight mentioned above\&. If the id line contains no asterisk then the weight defaults to 1\&.0\&. The alignment scoring system used is the same as for calculating complementarity among oligos (e\&.g\&. SELF\-ANY)\&. The remainder of an entry contains the sequence as lines following the id line up until a line starting with \*(Aq>\*(Aq or the end of the file\&. Whitespace and newlines are ignored\&. Characters \*(AqA\*(Aq, \*(AqT\*(Aq, \*(AqG\*(Aq, \*(AqC\*(Aq, \*(Aqa\*(Aq, \*(Aqt\*(Aq, \*(Aqg\*(Aq, \*(Aqc\*(Aq are retained and any other character is converted to \*(AqN\*(Aq (with the consequence that any IUB / IUPAC codes for ambiguous bases are converted to \*(AqN\*(Aq)\&. There are no restrictions on line length\&. An empty value for this parameter indicates that no library should be used\&.
+.RE
+.PP
+\fB\-mispriminglibraryfile\fR \fIinfile\fR
+.RS 4
+The name of a file containing a nucleotide sequence library of sequences to avoid amplifying (for example repetitive sequences, or possibly the sequences of genes in a gene family that should not be amplified\&.) The file must be in (a slightly restricted) FASTA format (W\&. B\&. Pearson and D\&.J\&. Lipman, PNAS 85:8 pp 2444\-2448 [1988]); we briefly discuss the organization of this file below\&. If this parameter is specified then Eprimer32 locally aligns each candidate primer against each library sequence and rejects those primers for which the local alignment score times a specified weight (see below) exceeds MAX\-MISPRIMING\&. (The maximum value of the weight is arbitrarily set to 100\&.0\&.) Each sequence entry in the FASTA\-format file must begin with an \*(Aqid line\*(Aq that starts with \*(Aq>\*(Aq\&. The contents of the id line is \*(Aqslightly restricted\*(Aq in that Eprimer32 parses everything after any optional asterisk (\*(Aq*\*(Aq) as a floating point number to use as the weight mentioned above\&. If the id line contains no asterisk then the weight defaults to 1\&.0\&. The alignment scoring system used is the same as for calculating complementarity among oligos (e\&.g\&. SELF\-ANY)\&. The remainder of an entry contains the sequence as lines following the id line up until a line starting with \*(Aq>\*(Aq or the end of the file\&. Whitespace and newlines are ignored\&. Characters \*(AqA\*(Aq, \*(AqT\*(Aq, \*(AqG\*(Aq, \*(AqC\*(Aq, \*(Aqa\*(Aq, \*(Aqt\*(Aq, \*(Aqg\*(Aq, \*(Aqc\*(Aq are retained and any other character is converted to \*(AqN\*(Aq (with the consequence that any IUB / IUPAC codes for ambiguous bases are converted to \*(AqN\*(Aq)\&. There are no restrictions on line length\&. An empty value for this parameter indicates that no repeat library should be used\&.
+.RE
+.SS "Additional section"
+.SS "Program options"
+.PP
+\fB\-numreturn\fR \fIinteger\fR
+.RS 4
+The maximum number of primer pairs to return\&. Primer pairs returned are sorted by their \*(Aqquality\*(Aq, in other words by the value of the objective function (where a lower number indicates a better primer pair)\&. Caution: setting this parameter to a large value will increase running time\&. Default value: 5
+.RE
+.SS "Sequence options"
+.PP
+\fB\-includedregion\fR \fIrange\fR
+.RS 4
+A sub\-region of the given sequence in which to pick primers\&. For example, often the first dozen or so bases of a sequence are vector, and should be excluded from consideration\&. The value for this parameter has the form (start),(end) where (start) is the index of the first base to consider, and (end) is the last in the primer\-picking region\&.
+.RE
+.PP
+\fB\-targetregion\fR \fIrange\fR
+.RS 4
+If one or more Targets is specified then a legal primer pair must flank at least one of them\&. A Target might be a simple sequence repeat site (for example a CA repeat) or a single\-base\-pair polymorphism\&. The value should be a space\-separated list of (start),(end) pairs where (start) is the index of the first base of a Target, and (end) is the last E\&.g\&. 50,51 requires primers to surround the 2 bases at positions 50 and 51\&.
+.RE
+.PP
+\fB\-excludedregion\fR \fIrange\fR
+.RS 4
+Primer oligos may not overlap any region specified in this tag\&. The associated value must be a space\-separated list of (start),(end) pairs where (start) is the index of the first base of the excluded region, and and (end) is the last\&. This tag is useful for tasks such as excluding regions of low sequence quality or for excluding regions containing repetitive elements such as ALUs or LINEs\&. E\&.g\&. 401,407 68,70 forbids selection of primers in the 7 bases starting at 401 and the 3 bases at 68\&.
+.RE
+.PP
+\fB\-forwardinput\fR \fIstring\fR
+.RS 4
+The sequence of a forward primer to check and around which to design reverse primers and optional internal oligos\&. Must be a substring of SEQUENCE\&.
+.RE
+.PP
+\fB\-reverseinput\fR \fIstring\fR
+.RS 4
+The sequence of a reverse primer to check and around which to design forward primers and optional internal oligos\&. Must be a substring of the reverse strand of SEQUENCE\&.
+.RE
+.SS "Primer options"
+.PP
+\fB\-gcclamp\fR \fIinteger\fR
+.RS 4
+Require the specified number of consecutive Gs and Cs at the 3\*(Aq end of both the forward and reverse primer\&. (This parameter has no effect on the internal oligo if one is requested\&.)
+.RE
+.PP
+\fB\-osize\fR \fIinteger\fR
+.RS 4
+Optimum length (in bases) of a primer oligo\&. Eprimer32 will attempt to pick primers close to this length\&. Default value: 20
+.RE
+.PP
+\fB\-minsize\fR \fIinteger\fR
+.RS 4
+Minimum acceptable length of a primer\&. Must be greater than 0 and less than or equal to MAX\-SIZE\&. Default value: 18
+.RE
+.PP
+\fB\-maxsize\fR \fIinteger\fR
+.RS 4
+Maximum acceptable length (in bases) of a primer\&. Currently this parameter cannot be larger than 35\&. This limit is governed by the maximum oligo size for which Eprimer32\*(Aqs melting\-temperature is valid\&. Default value: 27
+.RE
+.PP
+\fB\-otm\fR \fIfloat\fR
+.RS 4
+Optimum melting temperature(Celsius) for a primer oligo\&. Eprimer32 will try to pick primers with melting temperatures are close to this temperature\&. The oligo melting temperature formula in Eprimer32 is that given in Rychlik, Spencer and Rhoads, Nucleic Acids Research, vol 18, num 21, pp 6409\-6412 and Breslauer, Frank, Bloecker and Marky, Proc\&. Natl\&. Acad\&. Sci\&. USA, vol 83, pp 3746\-3750\&. Please refer to the former paper for background discussion\&. Default value: 60\&.0
+.RE
+.PP
+\fB\-mintm\fR \fIfloat\fR
+.RS 4
+Minimum acceptable melting temperature(Celsius) for a primer oligo\&. Default value: 57\&.0
+.RE
+.PP
+\fB\-maxtm\fR \fIfloat\fR
+.RS 4
+Maximum acceptable melting temperature(Celsius) for a primer oligo\&. Default value: 63\&.0
+.RE
+.PP
+\fB\-maxdifftm\fR \fIfloat\fR
+.RS 4
+Maximum acceptable (unsigned) difference between the melting temperatures of the forward and reverse primers\&. Default value: 100\&.0
+.RE
+.PP
+\fB\-ogcpercent\fR \fIfloat\fR
+.RS 4
+Primer optimum GC percent\&. Default value: 50\&.0
+.RE
+.PP
+\fB\-mingc\fR \fIfloat\fR
+.RS 4
+Minimum allowable percentage of Gs and Cs in any primer\&. Default value: 20\&.0
+.RE
+.PP
+\fB\-maxgc\fR \fIfloat\fR
+.RS 4
+Maximum allowable percentage of Gs and Cs in any primer generated by Primer\&. Default value: 80\&.0
+.RE
+.PP
+\fB\-saltconc\fR \fIfloat\fR
+.RS 4
+The millimolar concentration of salt (usually KCl) in the PCR\&. Eprimer32 uses this argument to calculate oligo melting temperatures\&. Default value: 50\&.0
+.RE
+.PP
+\fB\-dnaconc\fR \fIfloat\fR
+.RS 4
+The nanomolar concentration of annealing oligos in the PCR\&. Eprimer32 uses this argument to calculate oligo melting temperatures\&. The default (50nM) works well with the standard protocol used at the Whitehead/MIT Center for Genome Research\-\-0\&.5 microliters of 20 micromolar concentration for each primer oligo in a 20 microliter reaction with 10 nanograms template, 0\&.025 units/microliter Taq polymerase in 0\&.1 mM each dNTP, 1\&.5mM MgCl2, 50mM KCl, 10mM Tris\-HCL (pH 9\&.3) using 35 cycles with an annealing temperature of 56 degrees Celsius\&. This parameter corresponds to \*(Aqc\*(Aq in Rychlik, Spencer and Rhoads\*(Aq equation (ii) (Nucleic Acids Research, vol 18, num 21) where a suitable value (for a lower initial concentration of template) is \*(Aqempirically determined\*(Aq\&. The value of this parameter is less than the actual concentration of oligos in the reaction because it is the concentration of annealing oligos, which in turn depends on the amount of template (including PCR product) in a given cycle\&. This concentration increases a great deal during a PCR; fortunately PCR seems quite robust for a variety of oligo melting temperatures\&. See ADVICE FOR PICKING PRIMERS\&. Default value: 50\&.0
+.RE
+.PP
+\fB\-maxpolyx\fR \fIinteger\fR
+.RS 4
+The maximum allowable length of a mononucleotide repeat in a primer, for example AAAAAA\&. Default value: 5
+.RE
+.SS "Product options"
+.PP
+\fB\-psizeopt\fR \fIinteger\fR
+.RS 4
+The optimum size for the PCR product\&. 0 indicates that there is no optimum product size\&. Default value: 200
+.RE
+.PP
+\fB\-prange\fR \fIrange\fR
+.RS 4
+The associated values specify the lengths of the product that the user wants the primers to create, and is a space separated list of elements of the form (x)\-(y) where an (x)\-(y) pair is a legal range of lengths for the product\&. For example, if one wants PCR products to be between 100 to 150 bases (inclusive) then one would set this parameter to 100\-150\&. If one desires PCR products in either the range from 100 to 150 bases or in the range from 200 to 250 bases then one would set this parameter to 100\-150 200\-250\&. Eprimer32 favours ranges to the left side of the parameter string\&. Eprimer32 will return legal primers pairs in the first range regardless the value of the objective function for these pairs\&. Only if there are an insufficient number of primers in the first range will Eprimer32 return primers in a subsequent range\&. Default value: 100\-300
+.RE
+.PP
+\fB\-ptmopt\fR \fIfloat\fR
+.RS 4
+The optimum melting temperature for the PCR product\&. 0 indicates that there is no optimum temperature\&. Default value: 0\&.0
+.RE
+.PP
+\fB\-ptmmin\fR \fIfloat\fR
+.RS 4
+The minimum allowed melting temperature of the amplicon\&. Please see the documentation on the maximum melting temperature of the product for details\&. Default value: \-1000000\&.0
+.RE
+.PP
+\fB\-ptmmax\fR \fIfloat\fR
+.RS 4
+The maximum allowed melting temperature of the amplicon\&. Product Tm is calculated using the formula from Bolton and McCarthy, PNAS 84:1390 (1962) as presented in Sambrook, Fritsch and Maniatis, Molecular Cloning, p 11\&.46 (1989, CSHL Press)\&. Tm = 81\&.5 + 16\&.6(log10([Na+])) + \&.41*(%GC) \- 600/length Where [Na+} is the molar sodium concentration, (%GC) is the percent of Gs and Cs in the sequence, and length is the length of the sequence\&. A similar formula is used by the prime primer selection program in GCG, which instead uses 675\&.0/length in the last term (after F\&. Baldino, Jr, M\&.\-F\&. Chesselet, and M\&.E\&. Lewis, Methods in Enzymology 168:766 (1989) eqn (1) on page 766 without the mismatch and formamide terms)\&. The formulas here and in Baldino et al\&. assume Na+ rather than K+\&. According to J\&.G\&. Wetmur, Critical Reviews in BioChem\&. and Mol\&. Bio\&. 26:227 (1991) 50 mM K+ should be equivalent in these formulae to \&.2 M Na+\&. Eprimer32 uses the same salt concentration value for calculating both the primer melting temperature and the oligo melting temperature\&. If you are planning to use the PCR product for hybridization later this behavior will not give you the Tm under hybridization conditions\&. Default value: 1000000\&.0
+.RE
+.SS "Internal oligo input"
+.PP
+\fB\-oexcludedregion\fR \fIrange\fR
+.RS 4
+Middle oligos may not overlap any region specified by this tag\&. The associated value must be a space\-separated list of (start),(end) pairs, where (start) is the index of the first base of an excluded region, and (end) is the last\&. Often one would make Target regions excluded regions for internal oligos\&.
+.RE
+.PP
+\fB\-oligoinput\fR \fIstring\fR
+.RS 4
+The sequence of an internal oligo to check and around which to design forward and reverse primers\&. Must be a substring of SEQUENCE\&.
+.RE
+.SS "Internal oligo options"
+.PP
+\fB\-osizeopt\fR \fIinteger\fR
+.RS 4
+Optimum length (in bases) of an internal oligo\&. Eprimer32 will attempt to pick primers close to this length\&. Default value: 20
+.RE
+.PP
+\fB\-ominsize\fR \fIinteger\fR
+.RS 4
+Minimum acceptable length of an internal oligo\&. Must be greater than 0 and less than or equal to INTERNAL\-OLIGO\-MAX\-SIZE\&. Default value: 18
+.RE
+.PP
+\fB\-omaxsize\fR \fIinteger\fR
+.RS 4
+Maximum acceptable length (in bases) of an internal oligo\&. Currently this parameter cannot be larger than 35\&. This limit is governed by maximum oligo size for which Eprimer32\*(Aqs melting\-temperature is valid\&. Default value: 27
+.RE
+.PP
+\fB\-otmopt\fR \fIfloat\fR
+.RS 4
+Optimum melting temperature (Celsius) for an internal oligo\&. Eprimer32 will try to pick oligos with melting temperatures that are close to this temperature\&. The oligo melting temperature formula in Eprimer32 is that given in Rychlik, Spencer and Rhoads, Nucleic Acids Research, vol 18, num 21, pp 6409\-6412 and Breslauer, Frank, Bloecker and Marky, Proc\&. Natl\&. Acad\&. Sci\&. USA, vol 83, pp 3746\-3750\&. Please refer to the former paper for background discussion\&. Default value: 60\&.0
+.RE
+.PP
+\fB\-otmmin\fR \fIfloat\fR
+.RS 4
+Minimum acceptable melting temperature(Celsius) for an internal oligo\&. Default value: 57\&.0
+.RE
+.PP
+\fB\-otmmax\fR \fIfloat\fR
+.RS 4
+Maximum acceptable melting temperature (Celsius) for an internal oligo\&. Default value: 63\&.0
+.RE
+.PP
+\fB\-ogcopt\fR \fIfloat\fR
+.RS 4
+Internal oligo optimum GC percent\&. Default value: 50\&.0
+.RE
+.PP
+\fB\-ogcmin\fR \fIfloat\fR
+.RS 4
+Minimum allowable percentage of Gs and Cs in an internal oligo\&. Default value: 20\&.0
+.RE
+.PP
+\fB\-ogcmax\fR \fIfloat\fR
+.RS 4
+Maximum allowable percentage of Gs and Cs in any internal oligo generated by Primer\&. Default value: 80\&.0
+.RE
+.PP
+\fB\-osaltconc\fR \fIfloat\fR
+.RS 4
+The millimolar concentration of salt (usually KCl) in the hybridization\&. Eprimer32 uses this argument to calculate internal oligo melting temperatures\&. Default value: 50\&.0
+.RE
+.PP
+\fB\-odnaconc\fR \fIfloat\fR
+.RS 4
+The nanomolar concentration of annealing internal oligo in the hybridization\&. Default value: 50\&.0
+.RE
+.PP
+\fB\-oanyself\fR \fIfloat\fR
+.RS 4
+The maximum allowable local alignment score when testing an internal oligo for (local) self\-complementarity\&. Local self\-complementarity is taken to predict the tendency of oligos to anneal to themselves The scoring system gives 1\&.00 for complementary bases, \-0\&.25 for a match of any base (or N) with an N, \-1\&.00 for a mismatch, and \-2\&.00 for a gap\&. Only single\-base\-pair gaps are allowed\&. For example, the alignment 5\*(Aq ATCGNA 3\*(Aq || | | 3\*(Aq TA\-CGT 5\*(Aq is allowed (and yields a score of 1\&.75), but the alignment 5\*(Aq ATCCGNA 3\*(Aq || | | 3\*(Aq TA\-\-CGT 5\*(Aq is not considered\&. Scores are non\-negative, and a score of 0\&.00 indicates that there is no reasonable local alignment between two oligos\&. Default value: 12\&.00
+.RE
+.PP
+\fB\-oendself\fR \fIfloat\fR
+.RS 4
+The maximum allowable 3\*(Aq\-anchored global alignment score when testing a single oligo for self\-complementarity\&. The scoring system is as for the Maximum Complementarity argument\&. In the examples above the scores are 7\&.00 and 6\&.00 respectively\&. Scores are non\-negative, and a score of 0\&.00 indicates that there is no reasonable 3\*(Aq\-anchored global alignment between two oligos\&. In order to estimate 3\*(Aq\-anchored global alignments for candidate oligos, Primer assumes that the sequence from which to choose oligos is presented 5\*(Aq to 3\*(Aq\&. INTERNAL\-OLIGO\-SELF\-END is meaningless when applied to internal oligos used for hybridization\-based detection, since primer\-dimer will not occur\&. We recommend that INTERNAL\-OLIGO\-SELF\-END be set at least as high as INTERNAL\-OLIGO\-SELF\-ANY\&. Default value: 12\&.00
+.RE
+.PP
+\fB\-opolyxmax\fR \fIinteger\fR
+.RS 4
+The maximum allowable length of an internal oligo mononucleotide repeat, for example AAAAAA\&. Default value: 5
+.RE
+.PP
+\fB\-omishybmax\fR \fIfloat\fR
+.RS 4
+Similar to MAX\-MISPRIMING except that this parameter applies to the similarity of candidate internal oligos to the library specified in INTERNAL\-OLIGO\-MISHYB\-LIBRARY\&. Default value: 12\&.0
+.RE
+.SS "Advanced section"
+.PP
+\fB\-explainflag\fR \fIboolean\fR
+.RS 4
+If this flag is true, produce LEFT\-EXPLAIN, RIGHT\-EXPLAIN, and INTERNAL\-OLIGO\-EXPLAIN output tags, which are intended to provide information on the number of oligos and primer pairs that Eprimer32 examined, and statistics on the number discarded for various reasons\&. Default value: N
+.RE
+.PP
+\fB\-fileflag\fR \fIboolean\fR
+.RS 4
+If the associated value is true, then Eprimer32 creates two output files for each input SEQUENCE\&. File (sequence\-id)\&.for lists all acceptable forward primers for (sequence\-id), and (sequence\-id)\&.rev lists all acceptable reverse primers for (sequence\-id), where (sequence\-id) is the value of the SEQUENCE\-ID tag (which must be supplied)\&. In addition, if the input tag TASK is 1 or 4, Eprimer32 produces a file (sequence\-id)\&.int, which lists all acceptable internal oligos\&. Default value: N
+.RE
+.PP
+\fB\-firstbaseindex\fR \fIinteger\fR
+.RS 4
+This parameter is the index of the first base in the input sequence\&. For input and output using 1\-based indexing (such as that used in GenBank and to which many users are accustomed) set this parameter to 1\&. For input and output using 0\-based indexing set this parameter to 0\&. (This parameter also affects the indexes in the contents of the files produced when the primer file flag is set\&.) Default value: 1
+.RE
+.PP
+\fB\-pickanyway\fR \fIboolean\fR
+.RS 4
+If true pick a primer pair even if LEFT\-INPUT, RIGHT\-INPUT, or INTERNAL\-OLIGO\-INPUT violates specific constraints\&. Default value: N
+.RE
+.PP
+\fB\-maxmispriming\fR \fIfloat\fR
+.RS 4
+The maximum allowed weighted similarity with any sequence in MISPRIMING\-LIBRARY\&. Default value: 12\&.00
+.RE
+.PP
+\fB\-pairmaxmispriming\fR \fIfloat\fR
+.RS 4
+The maximum allowed sum of weighted similarities of a primer pair (one similarity for each primer) with any single sequence in MISPRIMING\-LIBRARY\&. Default value: 24\&.00
+.RE
+.PP
+\fB\-numnsaccepted\fR \fIinteger\fR
+.RS 4
+Maximum number of unknown bases (N) allowable in any primer\&.
+.RE
+.PP
+\fB\-selfany\fR \fIfloat\fR
+.RS 4
+The maximum allowable local alignment score when testing a single primer for (local) self\-complementarity and the maximum allowable local alignment score when testing for complementarity between forward and reverse primers\&. Local self\-complementarity is taken to predict the tendency of primers to anneal to each other without necessarily causing self\-priming in the PCR\&. The scoring system gives 1\&.00 for complementary bases, \-0\&.25 for a match of any base (or N) with an N, \-1\&.00 for a mismatch, and \-2\&.00 for a gap\&. Only single\-base\-pair gaps are allowed\&. For example, the alignment 5\*(Aq ATCGNA 3\*(Aq \&.\&.\&.|| | | 3\*(Aq TA\-CGT 5\*(Aq is allowed (and yields a score of 1\&.75), but the alignment 5\*(Aq ATCCGNA 3\*(Aq \&.\&.\&.|| | | 3\*(Aq TA\-\-CGT 5\*(Aq is not considered\&. Scores are non\-negative, and a score of 0\&.00 indicates that there is no reasonable local alignment between two oligos\&. Default value: 8\&.00
+.RE
+.PP
+\fB\-selfend\fR \fIfloat\fR
+.RS 4
+The maximum allowable 3\*(Aq\-anchored global alignment score when testing a single primer for self\-complementarity, and the maximum allowable 3\*(Aq\-anchored global alignment score when testing for complementarity between forward and reverse primers\&. The 3\*(Aq\-anchored global alignment score is taken to predict the likelihood of PCR\-priming primer\-dimers, for example 5\*(Aq ATGCCCTAGCTTCCGGATG 3\*(Aq \&.\&.\&.\&.\&.\&.\&.\&.\&.\&.\&.\&.\&.||| ||||| \&.\&.\&.\&.\&.\&.\&.\&.\&.\&.3\*(Aq AAGTCCTACATTTAGCCTAGT 5\*(Aq or 5\*(Aq AGGCTATGGGCCTCGCGA 3\*(Aq \&.\&.\&.\&.\&.\&.\&.\&.\&.\&.\&.\&.\&.\&.\&.|||||| \&.\&.\&.\&.\&.\&.\&.\&.\&.\&.\&.\&.3\*(Aq AGCGCTCCGGGTATCGGA 5\*(Aq The scoring system is as for the Maximum Complementarity argument\&. In the examples above the scores are 7\&.00 and 6\&.00 respectively\&. Scores are non\-negative, and a score of 0\&.00 indicates that there is no reasonable 3\*(Aq\-anchored global alignment between two oligos\&. In order to estimate 3\*(Aq\-anchored global alignments for candidate primers and primer pairs, Primer assumes that the sequence from which to choose primers is presented 5\*(Aq to 3\*(Aq\&. It is nonsensical to provide a larger value for this parameter than for the Maximum (local) Complementarity parameter because the score of a local alignment will always be at least as great as the score of a global alignment\&. Default value: 3\&.00
+.RE
+.PP
+\fB\-scorrection\fR \fIlist\fR
+.RS 4
+Specifies the salt correction formula for the melting temperature calculation\&. Default value: 1
+.RE
+.PP
+\fB\-tmformula\fR \fIlist\fR
+.RS 4
+Specifies details of melting temperature calculation\&. Default value: 1
+.RE
+.SS "Primer penalty weights"
+.PP
+\fB\-maxendstability\fR \fIfloat\fR
+.RS 4
+The maximum stability for the five 3\*(Aq bases of a forward or reverse primer\&. Bigger numbers mean more stable 3\*(Aq ends\&. The value is the maximum delta G for duplex disruption for the five 3\*(Aq bases as calculated using the nearest neighbor parameters published in Breslauer, Frank, Bloecker and Marky, Proc\&. Natl\&. Acad\&. Sci\&. USA, vol 83, pp 3746\-3750\&. Eprimer32 uses a completely permissive default value for backward compatibility (which we may change in the next release)\&. Rychlik recommends a maximum value of 9 (Wojciech Rychlik, \*(AqSelection of Primers for Polymerase Chain Reaction\*(Aq in BA White, Ed\&., \*(AqMethods in Molecular Biology, Vol\&. 15: PCR Protocols: Current Methods and Applications\*(Aq, 1993, pp 31\-40, Humana Press, Totowa NJ)\&. Default value: 9\&.0
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+eprimer32 is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/dastest.1e
+++ emboss-6.4.0/debian/manpages/dastest.1e
@@ -0,0 +1,124 @@
+'\" t
+.\"     Title: DASTEST
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "DASTEST" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+dastest \- Return DAS sources from a DAS server or from the DAS registry
+.SH "SYNOPSIS"
+.HP \w'\fBdastest\fR\ 'u
+\fBdastest\fR [\fB\-sequencesourcesonly\ \fR\fB\fIboolean\fR\fR] [\fB\-entrypoints\ \fR\fB\fIboolean\fR\fR] [\fB\-showtestqueries\ \fR\fB\fIboolean\fR\fR] [\fB\-runtestqueries\ \fR\fB\fIboolean\fR\fR] \fB\-host\ \fR\fB\fIstring\fR\fR \fB\-path\ \fR\fB\fIstring\fR\fR \fB\-port\ \fR\fB\fIinteger\fR\fR \fB\-servername\ \fR\fB\fIstring\fR\fR \fB\-maxtests\ \fR\fB\fIinteger\fR\fR \fB\-maxfeatures\ \fR\fB\fIinteger\fR\fR \fB\-maxsegments\ \fR\fB\fIinteger\fR\fR [\fB\-outfile\ \fR\fB\fIoutfile\fR\fR]
+.HP \w'\fBdastest\fR\ 'u
+\fBdastest\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBdastest\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Display,Information" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.SS "Additional section"
+.PP
+\fB\-sequencesourcesonly\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-entrypoints\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-showtestqueries\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-runtestqueries\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.SS "Advanced section"
+.PP
+\fB\-host\fR \fIstring\fR
+.RS 4
+Default value: www\&.dasregistry\&.org
+.RE
+.PP
+\fB\-path\fR \fIstring\fR
+.RS 4
+Default value: /das
+.RE
+.PP
+\fB\-port\fR \fIinteger\fR
+.RS 4
+Default value: 80
+.RE
+.PP
+\fB\-servername\fR \fIstring\fR
+.RS 4
+Default value: das
+.RE
+.PP
+\fB\-maxtests\fR \fIinteger\fR
+.RS 4
+Default value: 80
+.RE
+.PP
+\fB\-maxfeatures\fR \fIinteger\fR
+.RS 4
+Default value: 80
+.RE
+.PP
+\fB\-maxsegments\fR \fIinteger\fR
+.RS 4
+Default value: 5
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+Default value: stdout
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+dastest is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/shuffleseq.1e
+++ emboss-6.4.0/debian/manpages/shuffleseq.1e
@@ -0,0 +1,76 @@
+'\" t
+.\"     Title: SHUFFLESEQ
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "SHUFFLESEQ" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+shuffleseq \- Shuffles a set of sequences maintaining composition
+.SH "SYNOPSIS"
+.HP \w'\fBshuffleseq\fR\ 'u
+\fBshuffleseq\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-shuffle\ \fR\fB\fIinteger\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR
+.HP \w'\fBshuffleseq\fR\ 'u
+\fBshuffleseq\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBshuffleseq\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Mutation,Protein:Mutation" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqall\fR
+.RS 4
+.RE
+.SS "Advanced section"
+.PP
+\fB\-shuffle\fR \fIinteger\fR
+.RS 4
+Default value: 1
+.RE
+.SS "Output section"
+.PP
+\fB\-outseq\fR \fIseqoutall\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+shuffleseq is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/extractfeat.1e
+++ emboss-6.4.0/debian/manpages/extractfeat.1e
@@ -0,0 +1,131 @@
+'\" t
+.\"     Title: EXTRACTFEAT
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "EXTRACTFEAT" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+extractfeat \- Extract features from sequence(s)
+.SH "SYNOPSIS"
+.HP \w'\fBextractfeat\fR\ 'u
+\fBextractfeat\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR [\fB\-before\ \fR\fB\fIinteger\fR\fR] [\fB\-after\ \fR\fB\fIinteger\fR\fR] [\fB\-source\ \fR\fB\fIstring\fR\fR] [\fB\-type\ \fR\fB\fIstring\fR\fR] [\fB\-sense\ \fR\fB\fIinteger\fR\fR] [\fB\-minscore\ \fR\fB\fIfloat\fR\fR] [\fB\-maxscore\ \fR\fB\fIfloat\fR\fR] [\fB\-tag\ \fR\fB\fIstring\fR\fR] [\fB\-value\ \fR\fB\fIstring\fR\fR] [\fB\-join\ \fR\fB\fIboolean\fR\fR] [\fB\-featinname\ \fR\fB\fIboolean\fR\fR] [\fB\-describe\ \fR\fB\fIstring\fR\fR] \fB\-outseq\ \fR\fB\fIseqout\fR\fR
+.HP \w'\fBextractfeat\fR\ 'u
+\fBextractfeat\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBextractfeat\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit,Feature tables" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqall\fR
+.RS 4
+.RE
+.SS "Additional section"
+.PP
+\fB\-before\fR \fIinteger\fR
+.RS 4
+If this value is greater than 0 then that number of bases or residues before the feature are included in the extracted sequence\&. This allows you to get the context of the feature\&. If this value is negative then the start of the extracted sequence will be this number of bases/residues before the end of the feature\&. So a value of \*(Aq10\*(Aq will start the extraction 10 bases/residues before the start of the sequence, and a value of \*(Aq\-10\*(Aq will start the extraction 10 bases/residues before the end of the feature\&. The output sequence will be padded with \*(AqN\*(Aq or \*(AqX\*(Aq characters if the sequence starts after the required start of the extraction\&.
+.RE
+.PP
+\fB\-after\fR \fIinteger\fR
+.RS 4
+If this value is greater than 0 then that number of bases or residues after the feature are included in the extracted sequence\&. This allows you to get the context of the feature\&. If this value is negative then the end of the extracted sequence will be this number of bases/residues after the start of the feature\&. So a value of \*(Aq10\*(Aq will end the extraction 10 bases/residues after the end of the sequence, and a value of \*(Aq\-10\*(Aq will end the extraction 10 bases/residues after the start of the feature\&. The output sequence will be padded with \*(AqN\*(Aq or \*(AqX\*(Aq characters if the sequence ends before the required end of the extraction\&.
+.RE
+.PP
+\fB\-source\fR \fIstring\fR
+.RS 4
+By default any feature source in the feature table is shown\&. You can set this to match any feature source you wish to show\&. The source name is usually either the name of the program that detected the feature or it is the feature table (eg: EMBL) that the feature came from\&. The source may be wildcarded by using \*(Aq*\*(Aq\&. If you wish to show more than one source, separate their names with the character \*(Aq|\*(Aq, eg: gene* | embl Default value: *
+.RE
+.PP
+\fB\-type\fR \fIstring\fR
+.RS 4
+By default every feature in the feature table is extracted\&. You can set this to be any feature type you wish to extract\&. See http://www\&.ebi\&.ac\&.uk/embl/WebFeat/ for a list of the EMBL feature types and see the Uniprot user manual in http://www\&.uniprot\&.org/manual/sequence_annotation for a list of the Uniprot feature types\&. The type may be wildcarded by using \*(Aq*\*(Aq\&. If you wish to extract more than one type, separate their names with the character \*(Aq|\*(Aq, eg: *UTR | intron Default value: *
+.RE
+.PP
+\fB\-sense\fR \fIinteger\fR
+.RS 4
+By default any feature type in the feature table is extracted\&. You can set this to match any feature sense you wish\&. 0 \- any sense, 1 \- forward sense, \-1 \- reverse sense
+.RE
+.PP
+\fB\-minscore\fR \fIfloat\fR
+.RS 4
+Minimum score of feature to extract (see also maxscore) Default value: 0\&.0
+.RE
+.PP
+\fB\-maxscore\fR \fIfloat\fR
+.RS 4
+Maximum score of feature to extract\&. If both minscore and maxscore are zero (the default), then any score is ignored Default value: 0\&.0
+.RE
+.PP
+\fB\-tag\fR \fIstring\fR
+.RS 4
+Tags are the types of extra values that a feature may have\&. For example in the EMBL feature table, a \*(AqCDS\*(Aq type of feature may have the tags \*(Aq/codon\*(Aq, \*(Aq/codon_start\*(Aq, \*(Aq/db_xref\*(Aq, \*(Aq/EC_number\*(Aq, \*(Aq/evidence\*(Aq, \*(Aq/exception\*(Aq, \*(Aq/function\*(Aq, \*(Aq/gene\*(Aq, \*(Aq/label\*(Aq, \*(Aq/map\*(Aq, \*(Aq/note\*(Aq, \*(Aq/number\*(Aq, \*(Aq/partial\*(Aq, \*(Aq/product\*(Aq, \*(Aq/protein_id\*(Aq, \*(Aq/pseudo\*(Aq, \*(Aq/standard_name\*(Aq, \*(Aq/translation\*(Aq, \*(Aq/transl_except\*(Aq, \*(Aq/transl_table\*(Aq, or \*(Aq/usedin\*(Aq\&. Some of these tags also have values, for example \*(Aq/gene\*(Aq can have the value of the gene name\&. By default any feature tag in the feature table is extracted\&. You can set this to match any feature tag you wish to show\&. The tag may be wildcarded by using \*(Aq*\*(Aq\&. If you wish to extract more than one tag, separate their names with the character \*(Aq|\*(Aq, eg: gene | label Default value: *
+.RE
+.PP
+\fB\-value\fR \fIstring\fR
+.RS 4
+Tag values are the values associated with a feature tag\&. Tags are the types of extra values that a feature may have\&. For example in the EMBL feature table, a \*(AqCDS\*(Aq type of feature may have the tags \*(Aq/codon\*(Aq, \*(Aq/codon_start\*(Aq, \*(Aq/db_xref\*(Aq, \*(Aq/EC_number\*(Aq, \*(Aq/evidence\*(Aq, \*(Aq/exception\*(Aq, \*(Aq/function\*(Aq, \*(Aq/gene\*(Aq, \*(Aq/label\*(Aq, \*(Aq/map\*(Aq, \*(Aq/note\*(Aq, \*(Aq/number\*(Aq, \*(Aq/partial\*(Aq, \*(Aq/product\*(Aq, \*(Aq/protein_id\*(Aq, \*(Aq/pseudo\*(Aq, \*(Aq/standard_name\*(Aq, \*(Aq/translation\*(Aq, \*(Aq/transl_except\*(Aq, \*(Aq/transl_table\*(Aq, or \*(Aq/usedin\*(Aq\&. Only some of these tags can have values, for example \*(Aq/gene\*(Aq can have the value of the gene name\&. By default any feature tag value in the feature table is shown\&. You can set this to match any feature tag value you wish to show\&. The tag value may be wildcarded by using \*(Aq*\*(Aq\&. If you wish to show more than one tag value, separate their names with a space or the character \*(Aq|\*(Aq, eg: pax* | 10 Default value: *
+.RE
+.SS "Output section"
+.PP
+\fB\-join\fR \fIboolean\fR
+.RS 4
+Some features, such as CDS (coding sequence) and mRNA are composed of introns concatenated together\&. There may be other forms of \*(Aqjoined\*(Aq sequence, depending on the feature table\&. If this option is set TRUE, then any group of these features will be output as a single sequence\&. If the \*(Aqbefore\*(Aq and \*(Aqafter\*(Aq qualifiers have been set, then only the sequence before the first feature and after the last feature are added\&. Default value: N
+.RE
+.PP
+\fB\-featinname\fR \fIboolean\fR
+.RS 4
+To aid you in identifying the type of feature that has been output, the type of feature is added to the start of the description of the output sequence\&. Sometimes the description of a sequence is lost in subsequent processing of the sequences file, so it is useful for the type to be a part of the sequence ID name\&. If you set this to be TRUE then the name is added to the ID name of the output sequence\&. Default value: N
+.RE
+.PP
+\fB\-describe\fR \fIstring\fR
+.RS 4
+To aid you in identifying some further properties of a feature that has been output, this lets you specify one or more tag names that should be added to the output sequence Description text, together with their values (if any)\&. For example, if this is set to be \*(Aqgene\*(Aq, then if any output feature has the tag (for example) \*(Aq/gene=BRCA1\*(Aq associated with it, then the text \*(Aq(gene=BRCA1)\*(Aq will be added to the Description line\&. Tags are the types of extra values that a feature may have\&. For example in the EMBL feature table, a \*(AqCDS\*(Aq type of feature may have the tags \*(Aq/codon\*(Aq, \*(Aq/codon_start\*(Aq, \*(Aq/db_xref\*(Aq, \*(Aq/EC_number\*(Aq, \*(Aq/evidence\*(Aq, \*(Aq/exception\*(Aq, \*(Aq/function\*(Aq, \*(Aq/gene\*(Aq, \*(Aq/label\*(Aq, \*(Aq/map\*(Aq, \*(Aq/note\*(Aq, \*(Aq/number\*(Aq, \*(Aq/partial\*(Aq, \*(Aq/product\*(Aq, \*(Aq/protein_id\*(Aq, \*(Aq/pseudo\*(Aq, \*(Aq/standard_name\*(Aq, \*(Aq/translation\*(Aq, \*(Aq/transl_except\*(Aq, \*(Aq/transl_table\*(Aq, or \*(Aq/usedin\*(Aq\&. Some of these tags also have values, for example \*(Aq/gene\*(Aq can have the value of the gene name\&. By default no feature tag is displayed\&. You can set this to match any feature tag you wish to show\&. The tag may be wildcarded by using \*(Aq*\*(Aq\&. If you wish to extract more than one tag, separate their names with the character \*(Aq|\*(Aq, eg: gene | label
+.RE
+.PP
+\fB\-outseq\fR \fIseqout\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+extractfeat is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/edamdef.1e
+++ emboss-6.4.0/debian/manpages/edamdef.1e
@@ -0,0 +1,87 @@
+'\" t
+.\"     Title: EDAMDEF
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "EDAMDEF" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+edamdef \- Find EDAM ontology terms by definition
+.SH "SYNOPSIS"
+.HP \w'\fBedamdef\fR\ 'u
+\fBedamdef\fR \fB\-query\ \fR\fB\fIstring\fR\fR [\fB\-namespace\ \fR\fB\fIlist\fR\fR] \fB\-subclasses\ \fR\fB\fIboolean\fR\fR \fB\-obsolete\ \fR\fB\fIboolean\fR\fR \fB\-edamdef\ \fR\fB\fIoutobo\fR\fR
+.HP \w'\fBedamdef\fR\ 'u
+\fBedamdef\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBedamdef\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Ontology:EDAM,Data retrieval:Ontology data" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-query\fR \fIstring\fR
+.RS 4
+.RE
+.SS "Additional section"
+.PP
+\fB\-namespace\fR \fIlist\fR
+.RS 4
+By default all terms are returned\&. Searches can be limited to one or a few namespaces\&. Default value: *
+.RE
+.SS "Advanced section"
+.PP
+\fB\-subclasses\fR \fIboolean\fR
+.RS 4
+Extend the query matches to include all terms which are specialisations (EDAM sub\-classes) of the matched type\&. Default value: N
+.RE
+.PP
+\fB\-obsolete\fR \fIboolean\fR
+.RS 4
+The default behaviour is to not use or return obsolete terms\&. This option if set will include all terms\&. Default value: N
+.RE
+.SS "Output section"
+.PP
+\fB\-edamdef\fR \fIoutobo\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+edamdef is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/dbget.1e
+++ emboss-6.4.0/debian/manpages/dbget.1e
@@ -0,0 +1,90 @@
+'\" t
+.\"     Title: DBGET
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "DBGET" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+dbget \- Retrieve database entries for a named database, data type and data identifier
+.SH "SYNOPSIS"
+.HP \w'\fBdbget\fR\ 'u
+\fBdbget\fR \fB\-database\ \fR\fB\fIstring\fR\fR \fB\-datatype\ \fR\fB\fIstring\fR\fR \fB\-identifier\ \fR\fB\fIstring\fR\fR [\fB\-outfile\ \fR\fB\fIoutfile\fR\fR] \fB\-outdir\ \fR\fB\fIoutdir\fR\fR
+.HP \w'\fBdbget\fR\ 'u
+\fBdbget\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBdbget\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Misc" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-database\fR \fIstring\fR
+.RS 4
+This is the name of a database from the catalogue of public databases in the EMBOSS data file DRCAT\&.dat\&. If you are unsure of the available databases use dbfind\&. If you have a database name but are not sure its valid, use isdbname\&.
+.RE
+.PP
+\fB\-datatype\fR \fIstring\fR
+.RS 4
+This is the name of a retrievable datatype from the catalogue of public databases in the EMBOSS data file DRCAT\&.dat\&. The names are terms from the \*(Aqdata\*(Aq branch of the EDAM ontology, http://edamontology\&.sourceforge\&.net/\&. If you are unsure of the available retrievable datatypes for a given database, use dbtellquery\&. If you have a datatype name but are not sure its valid, use isdbdata\&.
+.RE
+.PP
+\fB\-identifier\fR \fIstring\fR
+.RS 4
+This is a data identifier (e\&.g\&. a sequence accession number) that is used to specify the data (of type \*(Aqdatatype\*(Aq) to retrieve\&. If you\*(Aqre unsure of the data identifier(s) that are used for a given query (database/datatype) use dbtellquery\&. The types of data identifier are listed under the \*(AqData identifier\*(Aq branch of the EDAM ontology (http://edamontology\&.sourceforge\&.net/)\&. For example values, see the catalogue of public databases in the EMBOSS data file DRCAT\&.dat\&. If you have a data identifier but are unsure of its type, use idtell\&.
+.RE
+.SS "Required section"
+.SS "Additional section"
+.SS "Advanced section"
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+Default value: stdout
+.RE
+.PP
+\fB\-outdir\fR \fIoutdir\fR
+.RS 4
+Default value: \&.
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+dbget is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/whichdb.1e
+++ emboss-6.4.0/debian/manpages/whichdb.1e
@@ -0,0 +1,80 @@
+'\" t
+.\"     Title: WHICHDB
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "WHICHDB" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+whichdb \- Search all sequence databases for an entry and retrieve it
+.SH "SYNOPSIS"
+.HP \w'\fBwhichdb\fR\ 'u
+\fBwhichdb\fR \fB\-entry\ \fR\fB\fIstring\fR\fR \fB\-get\ \fR\fB\fItoggle\fR\fR \fB\-showall\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBwhichdb\fR\ 'u
+\fBwhichdb\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBwhichdb\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Data retrieval:Sequence data" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-entry\fR \fIstring\fR
+.RS 4
+.RE
+.SS "Output section"
+.PP
+\fB\-get\fR \fItoggle\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-showall\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+whichdb is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/nospace.1e
+++ emboss-6.4.0/debian/manpages/nospace.1e
@@ -0,0 +1,78 @@
+'\" t
+.\"     Title: NOSPACE
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "NOSPACE" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+nospace \- Remove whitespace from an ASCII text file
+.SH "SYNOPSIS"
+.HP \w'\fBnospace\fR\ 'u
+\fBnospace\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR [\fB\-menu\ \fR\fB\fIlist\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBnospace\fR\ 'u
+\fBnospace\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBnospace\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-infile\fR \fIinfile\fR
+.RS 4
+.RE
+.SS "Required section"
+.SS "Additional section"
+.PP
+\fB\-menu\fR \fIlist\fR
+.RS 4
+Default value: all
+.RE
+.SS "Advanced section"
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+nospace is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/patmattest.1e
+++ emboss-6.4.0/debian/manpages/patmattest.1e
@@ -0,0 +1,75 @@
+'\" t
+.\"     Title: PATMATTEST
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "PATMATTEST" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+patmattest \- Test of pattern matching
+.SH "SYNOPSIS"
+.HP \w'\fBpatmattest\fR\ 'u
+\fBpatmattest\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR \fB\-expression\ \fR\fB\fIstring\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBpatmattest\fR\ 'u
+\fBpatmattest\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBpatmattest\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Test" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIsequence\fR
+.RS 4
+.RE
+.PP
+\fB\-expression\fR \fIstring\fR
+.RS 4
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+Default value: stdout
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+patmattest is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/merger.1e
+++ emboss-6.4.0/debian/manpages/merger.1e
@@ -0,0 +1,94 @@
+'\" t
+.\"     Title: MERGER
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "MERGER" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+merger \- Merge two overlapping sequences
+.SH "SYNOPSIS"
+.HP \w'\fBmerger\fR\ 'u
+\fBmerger\fR \fB\-asequence\ \fR\fB\fIsequence\fR\fR \fB\-bsequence\ \fR\fB\fIsequence\fR\fR [\fB\-datafile\ \fR\fB\fImatrixf\fR\fR] [\fB\-gapopen\ \fR\fB\fIfloat\fR\fR] [\fB\-gapextend\ \fR\fB\fIfloat\fR\fR] \fB\-outfile\ \fR\fB\fIalign\fR\fR \fB\-outseq\ \fR\fB\fIseqout\fR\fR
+.HP \w'\fBmerger\fR\ 'u
+\fBmerger\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBmerger\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Alignment:Consensus" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-asequence\fR \fIsequence\fR
+.RS 4
+.RE
+.PP
+\fB\-bsequence\fR \fIsequence\fR
+.RS 4
+.RE
+.PP
+\fB\-datafile\fR \fImatrixf\fR
+.RS 4
+This is the scoring matrix file used when comparing sequences\&. By default it is the file \*(AqEBLOSUM62\*(Aq (for proteins) or the file \*(AqEDNAFULL\*(Aq (for nucleic sequences)\&. These files are found in the \*(Aqdata\*(Aq directory of the EMBOSS installation\&.
+.RE
+.SS "Additional section"
+.PP
+\fB\-gapopen\fR \fIfloat\fR
+.RS 4
+Default value: @($(acdprotein)? 50\&.0 : 50\&.0 )
+.RE
+.PP
+\fB\-gapextend\fR \fIfloat\fR
+.RS 4
+Default value: @($(acdprotein)? 5\&.0 : 5\&.0)
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIalign\fR
+.RS 4
+.RE
+.PP
+\fB\-outseq\fR \fIseqout\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+merger is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/megamerger.1e
+++ emboss-6.4.0/debian/manpages/megamerger.1e
@@ -0,0 +1,90 @@
+'\" t
+.\"     Title: MEGAMERGER
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "MEGAMERGER" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+megamerger \- Merge two large overlapping DNA sequences
+.SH "SYNOPSIS"
+.HP \w'\fBmegamerger\fR\ 'u
+\fBmegamerger\fR \fB\-asequence\ \fR\fB\fIsequence\fR\fR \fB\-bsequence\ \fR\fB\fIsequence\fR\fR \fB\-wordsize\ \fR\fB\fIinteger\fR\fR [\fB\-prefer\ \fR\fB\fIboolean\fR\fR] \fB\-outseq\ \fR\fB\fIseqout\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBmegamerger\fR\ 'u
+\fBmegamerger\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBmegamerger\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Alignment:Consensus" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-asequence\fR \fIsequence\fR
+.RS 4
+.RE
+.PP
+\fB\-bsequence\fR \fIsequence\fR
+.RS 4
+.RE
+.SS "Required section"
+.PP
+\fB\-wordsize\fR \fIinteger\fR
+.RS 4
+Default value: 20
+.RE
+.SS "Additional section"
+.PP
+\fB\-prefer\fR \fIboolean\fR
+.RS 4
+When a mismatch between the two sequence is discovered, one or other of the two sequences must be used to create the merged sequence over this mismatch region\&. The default action is to create the merged sequence using the sequence where the mismatch is closest to that sequence\*(Aqs centre\&. If this option is used, then the first sequence (seqa) will always be used in preference to the other sequence when there is a mismatch\&. Default value: N
+.RE
+.SS "Output section"
+.PP
+\fB\-outseq\fR \fIseqout\fR
+.RS 4
+.RE
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+megamerger is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/newseq.1e
+++ emboss-6.4.0/debian/manpages/newseq.1e
@@ -0,0 +1,86 @@
+'\" t
+.\"     Title: NEWSEQ
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "NEWSEQ" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+newseq \- Create a sequence file from a typed\-in sequence
+.SH "SYNOPSIS"
+.HP \w'\fBnewseq\fR\ 'u
+\fBnewseq\fR \fB\-name\ \fR\fB\fIstring\fR\fR \fB\-description\ \fR\fB\fIstring\fR\fR \fB\-type\ \fR\fB\fIlist\fR\fR \fB\-sequence\ \fR\fB\fIstring\fR\fR \fB\-outseq\ \fR\fB\fIseqout\fR\fR
+.HP \w'\fBnewseq\fR\ 'u
+\fBnewseq\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBnewseq\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-name\fR \fIstring\fR
+.RS 4
+The name of of the sequence should be a single word that you will use to identify the sequence\&. It should have no (or few) punctuation characters in it\&.
+.RE
+.PP
+\fB\-description\fR \fIstring\fR
+.RS 4
+Enter any description of the sequence that you require\&.
+.RE
+.PP
+\fB\-type\fR \fIlist\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-sequence\fR \fIstring\fR
+.RS 4
+The sequence itself\&. Because of the limitation of the operating system, you will only be able to type in a short sequence of (typically) 250 characters, or so\&. The keyboard will beep at you when you have reached this limit and you will not be able to press the RETURN/ENTER key until you have deleted a few characters\&.
+.RE
+.SS "Output section"
+.PP
+\fB\-outseq\fR \fIseqout\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+newseq is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/featcopy.1e
+++ emboss-6.4.0/debian/manpages/featcopy.1e
@@ -0,0 +1,70 @@
+'\" t
+.\"     Title: FEATCOPY
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "FEATCOPY" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+featcopy \- Reads and writes a feature table
+.SH "SYNOPSIS"
+.HP \w'\fBfeatcopy\fR\ 'u
+\fBfeatcopy\fR \fB\-features\ \fR\fB\fIfeatures\fR\fR \fB\-outfeat\ \fR\fB\fIfeatout\fR\fR
+.HP \w'\fBfeatcopy\fR\ 'u
+\fBfeatcopy\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBfeatcopy\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Data retrieval:Feature data,Edit" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-features\fR \fIfeatures\fR
+.RS 4
+.RE
+.SS "Output section"
+.PP
+\fB\-outfeat\fR \fIfeatout\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+featcopy is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/cai.1e
+++ emboss-6.4.0/debian/manpages/cai.1e
@@ -0,0 +1,75 @@
+'\" t
+.\"     Title: CAI
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "CAI" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+cai \- Calculate codon adaptation index
+.SH "SYNOPSIS"
+.HP \w'\fBcai\fR\ 'u
+\fBcai\fR \fB\-seqall\ \fR\fB\fIseqall\fR\fR \fB\-cfile\ \fR\fB\fIcodon\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBcai\fR\ 'u
+\fBcai\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBcai\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Codon usage" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-seqall\fR \fIseqall\fR
+.RS 4
+.RE
+.PP
+\fB\-cfile\fR \fIcodon\fR
+.RS 4
+Default value: Eyeast_cai\&.cut
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+cai is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/inforesidue.1e
+++ emboss-6.4.0/debian/manpages/inforesidue.1e
@@ -0,0 +1,84 @@
+'\" t
+.\"     Title: INFORESIDUE
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "INFORESIDUE" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+inforesidue \- Return information on a given amino acid residue
+.SH "SYNOPSIS"
+.HP \w'\fBinforesidue\fR\ 'u
+\fBinforesidue\fR \fB\-code\ \fR\fB\fIstring\fR\fR \fB\-aadata\ \fR\fB\fIdatafile\fR\fR \fB\-mwdata\ \fR\fB\fIdatafile\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBinforesidue\fR\ 'u
+\fBinforesidue\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBinforesidue\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Data retrieval:Chemistry data" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-code\fR \fIstring\fR
+.RS 4
+Enter IUPAC amino acids codes, e\&.g\&. A, C, D, E etc\&. Default value: ABCDEFGHIJKLMNOPQRSTUVWXYZ
+.RE
+.PP
+\fB\-aadata\fR \fIdatafile\fR
+.RS 4
+Amino acid properties Default value: Eamino\&.dat
+.RE
+.PP
+\fB\-mwdata\fR \fIdatafile\fR
+.RS 4
+Molecular weight data for amino acids Default value: Emolwt\&.dat
+.RE
+.SS "Required section"
+.SS "Additional section"
+.SS "Advanced section"
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+inforesidue is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/seqxref.1e
+++ emboss-6.4.0/debian/manpages/seqxref.1e
@@ -0,0 +1,73 @@
+'\" t
+.\"     Title: SEQXREF
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "SEQXREF" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+seqxref \- Retrieve all database cross\-references for a sequence entry
+.SH "SYNOPSIS"
+.HP \w'\fBseqxref\fR\ 'u
+\fBseqxref\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBseqxref\fR\ 'u
+\fBseqxref\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBseqxref\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Data retrieval:Sequence data" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqall\fR
+.RS 4
+.RE
+.SS "Required section"
+.SS "Additional section"
+.SS "Advanced section"
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+seqxref is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/servertell.1e
+++ emboss-6.4.0/debian/manpages/servertell.1e
@@ -0,0 +1,79 @@
+'\" t
+.\"     Title: SERVERTELL
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "SERVERTELL" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+servertell \- Display information about a public server
+.SH "SYNOPSIS"
+.HP \w'\fBservertell\fR\ 'u
+\fBservertell\fR \fB\-server\ \fR\fB\fIstring\fR\fR [\fB\-full\ \fR\fB\fIboolean\fR\fR] [\fB\-outfile\ \fR\fB\fIoutfile\fR\fR]
+.HP \w'\fBservertell\fR\ 'u
+\fBservertell\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBservertell\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Data resources" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-server\fR \fIstring\fR
+.RS 4
+The name of the database defined locally for use by EMBOSS\&.
+.RE
+.SS "Additional section"
+.PP
+\fB\-full\fR \fIboolean\fR
+.RS 4
+The default behaviour is to report for relevant databases only basic information from the EMBOSS database definition Default value: N
+.RE
+.SS "Advanced section"
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+Default value: stdout
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+servertell is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/entrailshtml.1e
+++ emboss-6.4.0/debian/manpages/entrailshtml.1e
@@ -0,0 +1,71 @@
+'\" t
+.\"     Title: ENTRAILSHTML
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "ENTRAILSHTML" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+entrailshtml \- Reports the internal structures in HTML
+.SH "SYNOPSIS"
+.HP \w'\fBentrailshtml\fR\ 'u
+\fBentrailshtml\fR \fB\-tables\ \fR\fB\fIlist\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBentrailshtml\fR\ 'u
+\fBentrailshtml\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBentrailshtml\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Misc" command group(s)\&.
+.SH "OPTIONS"
+.SS "required section"
+.PP
+\fB\-tables\fR \fIlist\fR
+.RS 4
+Default value: all
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+entrailshtml is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/dbtellquery.1e
+++ emboss-6.4.0/debian/manpages/dbtellquery.1e
@@ -0,0 +1,81 @@
+'\" t
+.\"     Title: DBTELLQUERY
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "DBTELLQUERY" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+dbtellquery \- Show possible queries of a database
+.SH "SYNOPSIS"
+.HP \w'\fBdbtellquery\fR\ 'u
+\fBdbtellquery\fR \fB\-database\ \fR\fB\fIstring\fR\fR [\fB\-outfile\ \fR\fB\fIoutfile\fR\fR] [\fB\-html\ \fR\fB\fIboolean\fR\fR]
+.HP \w'\fBdbtellquery\fR\ 'u
+\fBdbtellquery\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBdbtellquery\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Information" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-database\fR \fIstring\fR
+.RS 4
+The unique identifier of the database\&. These are listed in the EMBOSS data file DRCAT\&.dat (field names in parenthesis) and can be the recommended or official unique identifier (\*(AqID\*(Aq), the alternative identifier (\*(AqIDalt\*(Aq), or the accession number (\*(AqAcc\*(Aq) of the database\&. Any of these are acceptable\&. Official database identifiers and accession numbers are taken from http://www\&.uniprot\&.org/docs/dbxref where available\&. You can use dbfind to find databases by keyword and return unique identifiers and other information\&.
+.RE
+.SS "Required section"
+.SS "Additional section"
+.SS "Advanced section"
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+Default value: stdout
+.RE
+.SS "Html section"
+.PP
+\fB\-html\fR \fIboolean\fR
+.RS 4
+If you are sending the output to a file, this will format it for displaying as a table in a WWW document\&. Default value: N
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+dbtellquery is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/dan.1e
+++ emboss-6.4.0/debian/manpages/dan.1e
@@ -0,0 +1,145 @@
+'\" t
+.\"     Title: DAN
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "DAN" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+dan \- Calculates nucleic acid melting temperature
+.SH "SYNOPSIS"
+.HP \w'\fBdan\fR\ 'u
+\fBdan\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-windowsize\ \fR\fB\fIinteger\fR\fR \fB\-shiftincrement\ \fR\fB\fIinteger\fR\fR \fB\-dnaconc\ \fR\fB\fIfloat\fR\fR \fB\-saltconc\ \fR\fB\fIfloat\fR\fR [\fB\-product\ \fR\fB\fItoggle\fR\fR] \fB\-formamide\ \fR\fB\fIfloat\fR\fR \fB\-mismatch\ \fR\fB\fIfloat\fR\fR \fB\-prodlen\ \fR\fB\fIinteger\fR\fR [\fB\-thermo\ \fR\fB\fItoggle\fR\fR] \fB\-temperature\ \fR\fB\fIfloat\fR\fR \fB\-rna\ \fR\fB\fIboolean\fR\fR \fB\-plot\ \fR\fB\fItoggle\fR\fR \fB\-mintemp\ \fR\fB\fIfloat\fR\fR \fB\-graph\ \fR\fB\fIxygraph\fR\fR \fB\-outfile\ \fR\fB\fIreport\fR\fR
+.HP \w'\fBdan\fR\ 'u
+\fBdan\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBdan\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Properties,Nucleic:Composition" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqall\fR
+.RS 4
+.RE
+.SS "Required section"
+.PP
+\fB\-windowsize\fR \fIinteger\fR
+.RS 4
+The values of melting point and other thermodynamic properties of the sequence are determined by taking a short length of sequence known as a window and determining the properties of the sequence in that window\&. The window is incrementally moved along the sequence with the properties being calculated at each new position\&. Default value: 20
+.RE
+.PP
+\fB\-shiftincrement\fR \fIinteger\fR
+.RS 4
+This is the amount by which the window is moved at each increment in order to find the melting point and other properties along the sequence\&. Default value: 1
+.RE
+.PP
+\fB\-dnaconc\fR \fIfloat\fR
+.RS 4
+Default value: 50\&.
+.RE
+.PP
+\fB\-saltconc\fR \fIfloat\fR
+.RS 4
+Default value: 50\&.
+.RE
+.SS "Additional section"
+.SS "Product options"
+.PP
+\fB\-product\fR \fItoggle\fR
+.RS 4
+This prompts for percent formamide, percent of mismatches allowed and product length\&.
+.RE
+.PP
+\fB\-formamide\fR \fIfloat\fR
+.RS 4
+This specifies the percent formamide to be used in calculations (it is ignored unless \-product is used)\&. Default value: 0\&.
+.RE
+.PP
+\fB\-mismatch\fR \fIfloat\fR
+.RS 4
+This specifies the percent mismatch to be used in calculations (it is ignored unless \-product is used)\&. Default value: 0\&.
+.RE
+.PP
+\fB\-prodlen\fR \fIinteger\fR
+.RS 4
+This specifies the product length to be used in calculations (it is ignored unless \-product is used)\&. Default value: $(windowsize)
+.RE
+.SS "Thermodynamic options"
+.PP
+\fB\-thermo\fR \fItoggle\fR
+.RS 4
+Output the DeltaG, DeltaH and DeltaS values of the sequence windows to the output data file\&.
+.RE
+.PP
+\fB\-temperature\fR \fIfloat\fR
+.RS 4
+If \-thermo has been specified then this specifies the temperature at which to calculate the DeltaG, DeltaH and DeltaS values\&. Default value: 25\&.
+.RE
+.SS "Advanced section"
+.PP
+\fB\-rna\fR \fIboolean\fR
+.RS 4
+This specifies that the sequence is an RNA sequence and not a DNA sequence\&.
+.RE
+.SS "Output section"
+.PP
+\fB\-plot\fR \fItoggle\fR
+.RS 4
+If this is not specified then the file of output data is produced, else a plot of the melting point along the sequence is produced\&.
+.RE
+.PP
+\fB\-mintemp\fR \fIfloat\fR
+.RS 4
+Enter a minimum value for the temperature scale (y\-axis) of the plot\&. Default value: 55\&.
+.RE
+.PP
+\fB\-graph\fR \fIxygraph\fR
+.RS 4
+.RE
+.PP
+\fB\-outfile\fR \fIreport\fR
+.RS 4
+If a plot is not being produced then data on the melting point etc\&. in each window along the sequence is output to the file\&.
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+dan is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/restover.1e
+++ emboss-6.4.0/debian/manpages/restover.1e
@@ -0,0 +1,155 @@
+'\" t
+.\"     Title: RESTOVER
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "RESTOVER" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+restover \- Find restriction enzymes producing a specific overhang
+.SH "SYNOPSIS"
+.HP \w'\fBrestover\fR\ 'u
+\fBrestover\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-datafile\ \fR\fB\fIdatafile\fR\fR \fB\-mfile\ \fR\fB\fIdatafile\fR\fR \fB\-seqcomp\ \fR\fB\fIstring\fR\fR \fB\-min\ \fR\fB\fIinteger\fR\fR \fB\-max\ \fR\fB\fIinteger\fR\fR \fB\-single\ \fR\fB\fIboolean\fR\fR \fB\-threeprime\ \fR\fB\fIboolean\fR\fR \fB\-blunt\ \fR\fB\fIboolean\fR\fR \fB\-sticky\ \fR\fB\fIboolean\fR\fR \fB\-ambiguity\ \fR\fB\fIboolean\fR\fR \fB\-plasmid\ \fR\fB\fIboolean\fR\fR \fB\-methylation\ \fR\fB\fIboolean\fR\fR \fB\-commercial\ \fR\fB\fIboolean\fR\fR \fB\-html\ \fR\fB\fIboolean\fR\fR \fB\-limit\ \fR\fB\fIboolean\fR\fR \fB\-alphabetic\ \fR\fB\fIboolean\fR\fR \fB\-fragments\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBrestover\fR\ 'u
+\fBrestover\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBrestover\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Restriction" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqall\fR
+.RS 4
+.RE
+.PP
+\fB\-datafile\fR \fIdatafile\fR
+.RS 4
+.RE
+.PP
+\fB\-mfile\fR \fIdatafile\fR
+.RS 4
+Default value: Emethylsites\&.dat
+.RE
+.SS "Required section"
+.PP
+\fB\-seqcomp\fR \fIstring\fR
+.RS 4
+.RE
+.SS "Advanced section"
+.PP
+\fB\-min\fR \fIinteger\fR
+.RS 4
+Default value: 1
+.RE
+.PP
+\fB\-max\fR \fIinteger\fR
+.RS 4
+Default value: 2000000000
+.RE
+.PP
+\fB\-single\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-threeprime\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-blunt\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-sticky\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-ambiguity\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-plasmid\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-methylation\fR \fIboolean\fR
+.RS 4
+If this is set then RE recognition sites will not match methylated bases\&. Default value: N
+.RE
+.PP
+\fB\-commercial\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.SS "Output section"
+.PP
+\fB\-html\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-limit\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-alphabetic\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-fragments\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+restover is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/dbxgcg.1e
+++ emboss-6.4.0/debian/manpages/dbxgcg.1e
@@ -0,0 +1,120 @@
+'\" t
+.\"     Title: DBXGCG
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "DBXGCG" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+dbxgcg \- Index a GCG formatted database using b+tree indices
+.SH "SYNOPSIS"
+.HP \w'\fBdbxgcg\fR\ 'u
+\fBdbxgcg\fR \fB\-dbname\ \fR\fB\fIstring\fR\fR \fB\-dbresource\ \fR\fB\fIstring\fR\fR \fB\-idformat\ \fR\fB\fIlist\fR\fR \fB\-directory\ \fR\fB\fIdirectory\fR\fR \fB\-filenames\ \fR\fB\fIstring\fR\fR \fB\-fields\ \fR\fB\fIlist\fR\fR \fB\-compressed\ \fR\fB\fIboolean\fR\fR \fB\-release\ \fR\fB\fIstring\fR\fR \fB\-date\ \fR\fB\fIstring\fR\fR \fB\-exclude\ \fR\fB\fIstring\fR\fR \fB\-indexoutdir\ \fR\fB\fIoutdir\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBdbxgcg\fR\ 'u
+\fBdbxgcg\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBdbxgcg\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Database indexing" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-dbname\fR \fIstring\fR
+.RS 4
+.RE
+.PP
+\fB\-dbresource\fR \fIstring\fR
+.RS 4
+.RE
+.PP
+\fB\-idformat\fR \fIlist\fR
+.RS 4
+Default value: SWISS
+.RE
+.PP
+\fB\-directory\fR \fIdirectory\fR
+.RS 4
+Default value: \&.
+.RE
+.PP
+\fB\-filenames\fR \fIstring\fR
+.RS 4
+Default value: *\&.seq
+.RE
+.SS "Required section"
+.PP
+\fB\-fields\fR \fIlist\fR
+.RS 4
+Default value: id,acc
+.RE
+.PP
+\fB\-compressed\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.SS "Advanced section"
+.PP
+\fB\-release\fR \fIstring\fR
+.RS 4
+Default value: 0\&.0
+.RE
+.PP
+\fB\-date\fR \fIstring\fR
+.RS 4
+Default value: 00/00/00
+.RE
+.PP
+\fB\-exclude\fR \fIstring\fR
+.RS 4
+.RE
+.SS "Output section"
+.PP
+\fB\-indexoutdir\fR \fIoutdir\fR
+.RS 4
+Default value: \&.
+.RE
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+dbxgcg is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/iep.1e
+++ emboss-6.4.0/debian/manpages/iep.1e
@@ -0,0 +1,114 @@
+'\" t
+.\"     Title: IEP
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "IEP" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+iep \- Calculate the isoelectric point of proteins
+.SH "SYNOPSIS"
+.HP \w'\fBiep\fR\ 'u
+\fBiep\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR [\fB\-amino\ \fR\fB\fIinteger\fR\fR] [\fB\-carboxyl\ \fR\fB\fIinteger\fR\fR] [\fB\-termini\ \fR\fB\fIboolean\fR\fR] [\fB\-lysinemodified\ \fR\fB\fIinteger\fR\fR] [\fB\-disulphides\ \fR\fB\fIinteger\fR\fR] \fB\-step\ \fR\fB\fIfloat\fR\fR \fB\-plot\ \fR\fB\fItoggle\fR\fR \fB\-report\ \fR\fB\fItoggle\fR\fR \fB\-graph\ \fR\fB\fIxygraph\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBiep\fR\ 'u
+\fBiep\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBiep\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Protein:Properties,Display" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqall\fR
+.RS 4
+.RE
+.SS "Additional section"
+.PP
+\fB\-amino\fR \fIinteger\fR
+.RS 4
+Default value: 1
+.RE
+.PP
+\fB\-carboxyl\fR \fIinteger\fR
+.RS 4
+Default value: 1
+.RE
+.PP
+\fB\-termini\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-lysinemodified\fR \fIinteger\fR
+.RS 4
+.RE
+.PP
+\fB\-disulphides\fR \fIinteger\fR
+.RS 4
+.RE
+.SS "Advanced section"
+.PP
+\fB\-step\fR \fIfloat\fR
+.RS 4
+Default value: \&.5
+.RE
+.SS "Output section"
+.PP
+\fB\-plot\fR \fItoggle\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-report\fR \fItoggle\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-graph\fR \fIxygraph\fR
+.RS 4
+.RE
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+iep is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/ontocount.1e
+++ emboss-6.4.0/debian/manpages/ontocount.1e
@@ -0,0 +1,83 @@
+'\" t
+.\"     Title: ONTOCOUNT
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "ONTOCOUNT" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+ontocount \- Count ontology term(s)
+.SH "SYNOPSIS"
+.HP \w'\fBontocount\fR\ 'u
+\fBontocount\fR \fB\-oboterms\ \fR\fB\fIobo\fR\fR \fB\-subclasses\ \fR\fB\fIboolean\fR\fR \fB\-obsolete\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBontocount\fR\ 'u
+\fBontocount\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBontocount\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Ontology" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-oboterms\fR \fIobo\fR
+.RS 4
+.RE
+.SS "Additional section"
+.SS "Advanced section"
+.PP
+\fB\-subclasses\fR \fIboolean\fR
+.RS 4
+Extend the query matches to include all terms which are specialisations (sub\-classes) of the matched terms\&. Default value: N
+.RE
+.PP
+\fB\-obsolete\fR \fIboolean\fR
+.RS 4
+The default behaviour is to not use or return obsolete terms\&. This option if set will include all terms\&. Default value: N
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+Default value: stdout
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+ontocount is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/preg.1e
+++ emboss-6.4.0/debian/manpages/preg.1e
@@ -0,0 +1,74 @@
+'\" t
+.\"     Title: PREG
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "PREG" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+preg \- Regular expression search of protein sequence(s)
+.SH "SYNOPSIS"
+.HP \w'\fBpreg\fR\ 'u
+\fBpreg\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-pattern\ \fR\fB\fIregexp\fR\fR \fB\-outfile\ \fR\fB\fIreport\fR\fR
+.HP \w'\fBpreg\fR\ 'u
+\fBpreg\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBpreg\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Protein:Motifs" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqall\fR
+.RS 4
+.RE
+.PP
+\fB\-pattern\fR \fIregexp\fR
+.RS 4
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIreport\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+preg is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/silent.1e
+++ emboss-6.4.0/debian/manpages/silent.1e
@@ -0,0 +1,91 @@
+'\" t
+.\"     Title: SILENT
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "SILENT" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+silent \- Find restriction sites to insert (mutate) with no translation change
+.SH "SYNOPSIS"
+.HP \w'\fBsilent\fR\ 'u
+\fBsilent\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR \fB\-enzymes\ \fR\fB\fIstring\fR\fR \fB\-sshow\ \fR\fB\fIboolean\fR\fR \fB\-tshow\ \fR\fB\fIboolean\fR\fR \fB\-allmut\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIreport\fR\fR
+.HP \w'\fBsilent\fR\ 'u
+\fBsilent\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBsilent\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Restriction" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIsequence\fR
+.RS 4
+.RE
+.SS "Required section"
+.PP
+\fB\-enzymes\fR \fIstring\fR
+.RS 4
+Default value: all
+.RE
+.SS "Output section"
+.PP
+\fB\-sshow\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-tshow\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-allmut\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-outfile\fR \fIreport\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+silent is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/taxgetrank.1e
+++ emboss-6.4.0/debian/manpages/taxgetrank.1e
@@ -0,0 +1,83 @@
+'\" t
+.\"     Title: TAXGETRANK
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "TAXGETRANK" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+taxgetrank \- Get parents of taxon(s)
+.SH "SYNOPSIS"
+.HP \w'\fBtaxgetrank\fR\ 'u
+\fBtaxgetrank\fR \fB\-taxons\ \fR\fB\fItaxon\fR\fR \fB\-rank\ \fR\fB\fIlist\fR\fR \fB\-hidden\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIouttaxon\fR\fR
+.HP \w'\fBtaxgetrank\fR\ 'u
+\fBtaxgetrank\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBtaxgetrank\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Ontology:Taxonomy" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-taxons\fR \fItaxon\fR
+.RS 4
+.RE
+.SS "Required section"
+.PP
+\fB\-rank\fR \fIlist\fR
+.RS 4
+Multiple ranks can be specified, or \*(Aq*\*(Aq for all Default value: kingdom,phylum,class,order,family,genus,species
+.RE
+.SS "Additional section"
+.SS "Advanced section"
+.PP
+\fB\-hidden\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIouttaxon\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+taxgetrank is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/edialign.1e
+++ emboss-6.4.0/debian/manpages/edialign.1e
@@ -0,0 +1,135 @@
+'\" t
+.\"     Title: EDIALIGN
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "EDIALIGN" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+edialign \- Local multiple alignment of sequences
+.SH "SYNOPSIS"
+.HP \w'\fBedialign\fR\ 'u
+\fBedialign\fR \fB\-sequences\ \fR\fB\fIseqset\fR\fR \fB\-nucmode\ \fR\fB\fIlist\fR\fR \fB\-revcomp\ \fR\fB\fIboolean\fR\fR [\fB\-overlapw\ \fR\fB\fIselection\fR\fR] [\fB\-linkage\ \fR\fB\fIlist\fR\fR] [\fB\-maxfragl\ \fR\fB\fIinteger\fR\fR] \fB\-fragmat\ \fR\fB\fIboolean\fR\fR \fB\-fragsim\ \fR\fB\fIinteger\fR\fR [\fB\-itscore\ \fR\fB\fIboolean\fR\fR] [\fB\-threshold\ \fR\fB\fIfloat\fR\fR] \fB\-mask\ \fR\fB\fIboolean\fR\fR \fB\-dostars\ \fR\fB\fIboolean\fR\fR \fB\-starnum\ \fR\fB\fIinteger\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR
+.HP \w'\fBedialign\fR\ 'u
+\fBedialign\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBedialign\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Alignment:Multiple" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequences\fR \fIseqset\fR
+.RS 4
+.RE
+.SS "Additional section"
+.PP
+\fB\-nucmode\fR \fIlist\fR
+.RS 4
+Nucleic acid sequence alignment mode (simple, translated or mixed) Default value: n
+.RE
+.PP
+\fB\-revcomp\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-overlapw\fR \fIselection\fR
+.RS 4
+By default overlap weights are used when Nseq =<35 but you can set this to \*(Aqyes\*(Aq or \*(Aqno\*(Aq Default value: default (when Nseq =< 35)
+.RE
+.PP
+\fB\-linkage\fR \fIlist\fR
+.RS 4
+Clustering method to construct sequence tree (UPGMA, minimum linkage or maximum linkage) Default value: UPGMA
+.RE
+.PP
+\fB\-maxfragl\fR \fIinteger\fR
+.RS 4
+Default value: 40
+.RE
+.PP
+\fB\-fragmat\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-fragsim\fR \fIinteger\fR
+.RS 4
+Default value: 4
+.RE
+.PP
+\fB\-itscore\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-threshold\fR \fIfloat\fR
+.RS 4
+Default value: 0\&.0
+.RE
+.SS "Output section"
+.PP
+\fB\-mask\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-dostars\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-starnum\fR \fIinteger\fR
+.RS 4
+Default value: 4
+.RE
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.PP
+\fB\-outseq\fR \fIseqoutall\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+edialign is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/notab.1e
+++ emboss-6.4.0/debian/manpages/notab.1e
@@ -0,0 +1,73 @@
+'\" t
+.\"     Title: NOTAB
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "NOTAB" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+notab \- Replace tabs with spaces in an ASCII text file
+.SH "SYNOPSIS"
+.HP \w'\fBnotab\fR\ 'u
+\fBnotab\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBnotab\fR\ 'u
+\fBnotab\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBnotab\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-infile\fR \fIinfile\fR
+.RS 4
+.RE
+.SS "Required section"
+.SS "Additional section"
+.SS "Advanced section"
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+notab is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/drfindresource.1e
+++ emboss-6.4.0/debian/manpages/drfindresource.1e
@@ -0,0 +1,82 @@
+'\" t
+.\"     Title: DRFINDRESOURCE
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "DRFINDRESOURCE" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+drfindresource \- Find public databases by resource
+.SH "SYNOPSIS"
+.HP \w'\fBdrfindresource\fR\ 'u
+\fBdrfindresource\fR \fB\-query\ \fR\fB\fIstring\fR\fR \fB\-sensitive\ \fR\fB\fIboolean\fR\fR \fB\-subclasses\ \fR\fB\fIboolean\fR\fR \fB\-drfindresource\ \fR\fB\fIoutresource\fR\fR
+.HP \w'\fBdrfindresource\fR\ 'u
+\fBdrfindresource\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBdrfindresource\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Ontology:EDAM,Data retrieval:Resource data" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-query\fR \fIstring\fR
+.RS 4
+.RE
+.SS "Additional section"
+.SS "Advanced section"
+.PP
+\fB\-sensitive\fR \fIboolean\fR
+.RS 4
+By default, the query keywords are matched against the EDAM term names (and synonyms) only\&. This option also matches the keywords against the EDAM term definitions and will therefore (typically) report more matches\&. Default value: N
+.RE
+.PP
+\fB\-subclasses\fR \fIboolean\fR
+.RS 4
+Extend the query matches to include all terms which are specialisations (EDAM sub\-classes) of the matched type\&. Default value: Y
+.RE
+.SS "Output section"
+.PP
+\fB\-drfindresource\fR \fIoutresource\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+drfindresource is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/dotmatcher.1e
+++ emboss-6.4.0/debian/manpages/dotmatcher.1e
@@ -0,0 +1,99 @@
+'\" t
+.\"     Title: DOTMATCHER
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "DOTMATCHER" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+dotmatcher \- Draw a threshold dotplot of two sequences
+.SH "SYNOPSIS"
+.HP \w'\fBdotmatcher\fR\ 'u
+\fBdotmatcher\fR \fB\-asequence\ \fR\fB\fIsequence\fR\fR \fB\-bsequence\ \fR\fB\fIsequence\fR\fR [\fB\-matrixfile\ \fR\fB\fImatrix\fR\fR] [\fB\-windowsize\ \fR\fB\fIinteger\fR\fR] [\fB\-threshold\ \fR\fB\fIinteger\fR\fR] \fB\-stretch\ \fR\fB\fItoggle\fR\fR \fB\-graph\ \fR\fB\fIgraph\fR\fR \fB\-xygraph\ \fR\fB\fIxygraph\fR\fR
+.HP \w'\fBdotmatcher\fR\ 'u
+\fBdotmatcher\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBdotmatcher\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Alignment:Dot plots" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-asequence\fR \fIsequence\fR
+.RS 4
+.RE
+.PP
+\fB\-bsequence\fR \fIsequence\fR
+.RS 4
+.RE
+.PP
+\fB\-matrixfile\fR \fImatrix\fR
+.RS 4
+This is the scoring matrix file used when comparing sequences\&. By default it is the file \*(AqEBLOSUM62\*(Aq (for proteins) or the file \*(AqEDNAFULL\*(Aq (for nucleic sequences)\&. These files are found in the \*(Aqdata\*(Aq directory of the EMBOSS installation\&.
+.RE
+.SS "Additional section"
+.PP
+\fB\-windowsize\fR \fIinteger\fR
+.RS 4
+Default value: 10
+.RE
+.PP
+\fB\-threshold\fR \fIinteger\fR
+.RS 4
+Default value: 23
+.RE
+.SS "Output section"
+.PP
+\fB\-stretch\fR \fItoggle\fR
+.RS 4
+Display a non\-proportional graph Default value: N
+.RE
+.PP
+\fB\-graph\fR \fIgraph\fR
+.RS 4
+.RE
+.PP
+\fB\-xygraph\fR \fIxygraph\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+dotmatcher is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/ensembltest.1e
+++ emboss-6.4.0/debian/manpages/ensembltest.1e
@@ -0,0 +1,94 @@
+'\" t
+.\"     Title: ENSEMBLTEST
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "ENSEMBLTEST" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+ensembltest \- Demonstration of the Ensembl API to be\&.
+.SH "SYNOPSIS"
+.HP \w'\fBensembltest\fR\ 'u
+\fBensembltest\fR \fB\-large\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR \fB\-maxnum\ \fR\fB\fIinteger\fR\fR \fB\-exons\ \fR\fB\fIseqoutall\fR\fR \fB\-transcripts\ \fR\fB\fIseqoutall\fR\fR \fB\-translations\ \fR\fB\fIseqoutall\fR\fR
+.HP \w'\fBensembltest\fR\ 'u
+\fBensembltest\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBensembltest\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Test" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.SS "Required section"
+.SS "Additional section"
+.PP
+\fB\-large\fR \fIboolean\fR
+.RS 4
+Set this to \*(AqY\*(Aq to download large test data sets\&. Default value: N
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.PP
+\fB\-outseq\fR \fIseqoutall\fR
+.RS 4
+.RE
+.PP
+\fB\-maxnum\fR \fIinteger\fR
+.RS 4
+Default value: 25
+.RE
+.PP
+\fB\-exons\fR \fIseqoutall\fR
+.RS 4
+.RE
+.PP
+\fB\-transcripts\fR \fIseqoutall\fR
+.RS 4
+.RE
+.PP
+\fB\-translations\fR \fIseqoutall\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+ensembltest is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/infoseq.1e
+++ emboss-6.4.0/debian/manpages/infoseq.1e
@@ -0,0 +1,152 @@
+'\" t
+.\"     Title: INFOSEQ
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "INFOSEQ" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+infoseq \- Display basic information about sequences
+.SH "SYNOPSIS"
+.HP \w'\fBinfoseq\fR\ 'u
+\fBinfoseq\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-columns\ \fR\fB\fIboolean\fR\fR \fB\-delimiter\ \fR\fB\fIstring\fR\fR [\fB\-outfile\ \fR\fB\fIoutfile\fR\fR] [\fB\-html\ \fR\fB\fIboolean\fR\fR] \fB\-only\ \fR\fB\fIboolean\fR\fR \fB\-heading\ \fR\fB\fIboolean\fR\fR \fB\-usa\ \fR\fB\fIboolean\fR\fR \fB\-database\ \fR\fB\fIboolean\fR\fR \fB\-name\ \fR\fB\fIboolean\fR\fR \fB\-accession\ \fR\fB\fIboolean\fR\fR \fB\-gi\ \fR\fB\fIboolean\fR\fR \fB\-seqversion\ \fR\fB\fIboolean\fR\fR \fB\-type\ \fR\fB\fIboolean\fR\fR \fB\-length\ \fR\fB\fIboolean\fR\fR \fB\-pgc\ \fR\fB\fIboolean\fR\fR \fB\-organism\ \fR\fB\fIboolean\fR\fR \fB\-description\ \fR\fB\fIboolean\fR\fR
+.HP \w'\fBinfoseq\fR\ 'u
+\fBinfoseq\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBinfoseq\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Data retrieval:Sequence data" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqall\fR
+.RS 4
+.RE
+.SS "Advanced section"
+.PP
+\fB\-columns\fR \fIboolean\fR
+.RS 4
+Set this option on (Y) to print the sequence information into neat, aligned columns in the output file\&. Alternatively, leave it unset (N), in which case the information records will be delimited by a character, which you may specify by using the \-delimiter option\&. In other words, if \-columns is set on, the \-delimiter option is overriden\&. Default value: Y
+.RE
+.PP
+\fB\-delimiter\fR \fIstring\fR
+.RS 4
+This string, which is usually a single character only, is used to delimit individual records in the text output file\&. It could be a space character, a tab character, a pipe character or any other character or string\&. Default value: |
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+If you enter the name of a file here then this program will write the sequence details into that file\&. Default value: stdout
+.RE
+.PP
+\fB\-html\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-only\fR \fIboolean\fR
+.RS 4
+This is a way of shortening the command line if you only want a few things to be displayed\&. Instead of specifying: \*(Aq\-nohead \-noname \-noacc \-notype \-nopgc \-nodesc\*(Aq to get only the length output, you can specify \*(Aq\-only \-length\*(Aq Default value: N
+.RE
+.PP
+\fB\-heading\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-usa\fR \fIboolean\fR
+.RS 4
+Default value: @(!$(only))
+.RE
+.PP
+\fB\-database\fR \fIboolean\fR
+.RS 4
+Default value: @(!$(only))
+.RE
+.PP
+\fB\-name\fR \fIboolean\fR
+.RS 4
+Default value: @(!$(only))
+.RE
+.PP
+\fB\-accession\fR \fIboolean\fR
+.RS 4
+Default value: @(!$(only))
+.RE
+.PP
+\fB\-gi\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-seqversion\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-type\fR \fIboolean\fR
+.RS 4
+Default value: @(!$(only))
+.RE
+.PP
+\fB\-length\fR \fIboolean\fR
+.RS 4
+Default value: @(!$(only))
+.RE
+.PP
+\fB\-pgc\fR \fIboolean\fR
+.RS 4
+Default value: @(!$(only))
+.RE
+.PP
+\fB\-organism\fR \fIboolean\fR
+.RS 4
+Default value: @(!$(only))
+.RE
+.PP
+\fB\-description\fR \fIboolean\fR
+.RS 4
+Default value: @(!$(only))
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+infoseq is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/extractalign.1e
+++ emboss-6.4.0/debian/manpages/extractalign.1e
@@ -0,0 +1,76 @@
+'\" t
+.\"     Title: EXTRACTALIGN
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "EXTRACTALIGN" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+extractalign \- Extract regions from a sequence alignment
+.SH "SYNOPSIS"
+.HP \w'\fBextractalign\fR\ 'u
+\fBextractalign\fR \fB\-sequence\ \fR\fB\fIseqset\fR\fR \fB\-regions\ \fR\fB\fIrange\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR
+.HP \w'\fBextractalign\fR\ 'u
+\fBextractalign\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBextractalign\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Alignment,Data retrieval:Sequence data,Edit" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqset\fR
+.RS 4
+.RE
+.SS "Required section"
+.PP
+\fB\-regions\fR \fIrange\fR
+.RS 4
+Regions to extract\&. A set of regions is specified by a set of pairs of positions\&. The positions are integers\&. They are separated by any non\-digit, non\-alpha character\&. Examples of region specifications are: 24\-45, 56\-78 1:45, 67=99;765\&.\&.888 1,5,8,10,23,45,57,99 Default value: $(sequence\&.begin)\-$(sequence\&.end)
+.RE
+.SS "Output section"
+.PP
+\fB\-outseq\fR \fIseqoutall\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+extractalign is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/drget.1e
+++ emboss-6.4.0/debian/manpages/drget.1e
@@ -0,0 +1,72 @@
+'\" t
+.\"     Title: DRGET
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "DRGET" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+drget \- Get data resource entries
+.SH "SYNOPSIS"
+.HP \w'\fBdrget\fR\ 'u
+\fBdrget\fR \fB\-resources\ \fR\fB\fIresource\fR\fR \fB\-outfile\ \fR\fB\fIoutresource\fR\fR
+.HP \w'\fBdrget\fR\ 'u
+\fBdrget\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBdrget\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Data retrieval:Resource data" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-resources\fR \fIresource\fR
+.RS 4
+.RE
+.SS "Additional section"
+.SS "Advanced section"
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutresource\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+drget is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/fuzztran.1e
+++ emboss-6.4.0/debian/manpages/fuzztran.1e
@@ -0,0 +1,85 @@
+'\" t
+.\"     Title: FUZZTRAN
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "FUZZTRAN" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+fuzztran \- Search for patterns in protein sequences (translated)
+.SH "SYNOPSIS"
+.HP \w'\fBfuzztran\fR\ 'u
+\fBfuzztran\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-pattern\ \fR\fB\fIpattern\fR\fR [\fB\-frame\ \fR\fB\fIlist\fR\fR] [\fB\-table\ \fR\fB\fIlist\fR\fR] \fB\-outfile\ \fR\fB\fIreport\fR\fR
+.HP \w'\fBfuzztran\fR\ 'u
+\fBfuzztran\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBfuzztran\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Motifs,Protein:Motifs" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqall\fR
+.RS 4
+.RE
+.PP
+\fB\-pattern\fR \fIpattern\fR
+.RS 4
+The standard IUPAC one\-letter codes for the amino acids are used\&. The symbol \*(Aqx\*(Aq is used for a position where any amino acid is accepted\&. Ambiguities are indicated by listing the acceptable amino acids for a given position, between square parentheses \*(Aq[ ]\*(Aq\&. For example: [ALT] stands for Ala or Leu or Thr\&. Ambiguities are also indicated by listing between a pair of curly brackets \*(Aq{ }\*(Aq the amino acids that are not accepted at a gven position\&. For example: {AM} stands for any amino acid except Ala and Met\&. Each element in a pattern is separated from its neighbor by a \*(Aq\-\*(Aq\&. (Optional in fuzztran) Repetition of an element of the pattern can be indicated by following that element with a numerical value or a numerical range between parenthesis\&. Examples: x(3) corresponds to x\-x\-x, x(2,4) corresponds to x\-x or x\-x\-x or x\-x\-x\-x\&. When a pattern is restricted to either the N\- or C\-terminal of a sequence, that pattern either starts with a \*(Aq<\*(Aq symbol or respectively ends with a \*(Aq>\*(Aq symbol\&. A period ends the pattern\&. (Optional in fuzztran)\&. For example, [DE](2)HS{P}X(2)PX(2,4)C
+.RE
+.SS "Additional section"
+.PP
+\fB\-frame\fR \fIlist\fR
+.RS 4
+Default value: 1
+.RE
+.PP
+\fB\-table\fR \fIlist\fR
+.RS 4
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIreport\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+fuzztran is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/backtranseq.1e
+++ emboss-6.4.0/debian/manpages/backtranseq.1e
@@ -0,0 +1,75 @@
+'\" t
+.\"     Title: BACKTRANSEQ
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "BACKTRANSEQ" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+backtranseq \- Back\-translate a protein sequence to a nucleotide sequence
+.SH "SYNOPSIS"
+.HP \w'\fBbacktranseq\fR\ 'u
+\fBbacktranseq\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR [\fB\-cfile\ \fR\fB\fIcodon\fR\fR] \fB\-outfile\ \fR\fB\fIseqoutall\fR\fR
+.HP \w'\fBbacktranseq\fR\ 'u
+\fBbacktranseq\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBbacktranseq\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Translation,Protein:Composition" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqall\fR
+.RS 4
+.RE
+.PP
+\fB\-cfile\fR \fIcodon\fR
+.RS 4
+Default value: Ehuman\&.cut
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIseqoutall\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+backtranseq is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/sixpack.1e
+++ emboss-6.4.0/debian/manpages/sixpack.1e
@@ -0,0 +1,155 @@
+'\" t
+.\"     Title: SIXPACK
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "SIXPACK" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+sixpack \- Display a DNA sequence with 6\-frame translation and ORFs
+.SH "SYNOPSIS"
+.HP \w'\fBsixpack\fR\ 'u
+\fBsixpack\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR [\fB\-table\ \fR\fB\fIlist\fR\fR] [\fB\-firstorf\ \fR\fB\fIboolean\fR\fR] [\fB\-lastorf\ \fR\fB\fIboolean\fR\fR] [\fB\-mstart\ \fR\fB\fIboolean\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR \fB\-reverse\ \fR\fB\fIboolean\fR\fR \fB\-orfminsize\ \fR\fB\fIinteger\fR\fR \fB\-uppercase\ \fR\fB\fIrange\fR\fR \fB\-highlight\ \fR\fB\fIrange\fR\fR \fB\-number\ \fR\fB\fIboolean\fR\fR \fB\-width\ \fR\fB\fIinteger\fR\fR \fB\-length\ \fR\fB\fIinteger\fR\fR \fB\-margin\ \fR\fB\fIinteger\fR\fR \fB\-name\ \fR\fB\fIboolean\fR\fR \fB\-description\ \fR\fB\fIboolean\fR\fR \fB\-offset\ \fR\fB\fIinteger\fR\fR \fB\-html\ \fR\fB\fIboolean\fR\fR
+.HP \w'\fBsixpack\fR\ 'u
+\fBsixpack\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBsixpack\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Gene finding,Nucleic:Translation,Display" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIsequence\fR
+.RS 4
+.RE
+.SS "Additional section"
+.PP
+\fB\-table\fR \fIlist\fR
+.RS 4
+Genetics code used for the translation
+.RE
+.PP
+\fB\-firstorf\fR \fIboolean\fR
+.RS 4
+Count the beginning of a sequence as a possible ORF, even if it\*(Aqs inferior to the minimal ORF size\&. Default value: Y
+.RE
+.PP
+\fB\-lastorf\fR \fIboolean\fR
+.RS 4
+Count the end of a sequence as a possible ORF, even if it\*(Aqs not finishing with a STOP, or inferior to the minimal ORF size\&. Default value: Y
+.RE
+.PP
+\fB\-mstart\fR \fIboolean\fR
+.RS 4
+Displays only ORFs starting with an M\&. Default value: N
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.PP
+\fB\-outseq\fR \fIseqoutall\fR
+.RS 4
+ORF sequence output
+.RE
+.PP
+\fB\-reverse\fR \fIboolean\fR
+.RS 4
+Display also the translation of the DNA sequence in the 3 reverse frames Default value: Y
+.RE
+.PP
+\fB\-orfminsize\fR \fIinteger\fR
+.RS 4
+Minimum size of Open Reading Frames (ORFs) to display in the translations\&. Default value: 1
+.RE
+.PP
+\fB\-uppercase\fR \fIrange\fR
+.RS 4
+Regions to put in uppercase\&. If this is left blank, then the sequence case is left alone\&. A set of regions is specified by a set of pairs of positions\&. The positions are integers\&. They are separated by any non\-digit, non\-alpha character\&. Examples of region specifications are: 24\-45, 56\-78 1:45, 67=99;765\&.\&.888 1,5,8,10,23,45,57,99
+.RE
+.PP
+\fB\-highlight\fR \fIrange\fR
+.RS 4
+Regions to colour if formatting for HTML\&. If this is left blank, then the sequence is left alone\&. A set of regions is specified by a set of pairs of positions\&. The positions are integers\&. They are followed by any valid HTML font colour\&. Examples of region specifications are: 24\-45 blue 56\-78 orange 1\-100 green 120\-156 red A file of ranges to colour (one range per line) can be specified as \*(Aq@filename\*(Aq\&.
+.RE
+.PP
+\fB\-number\fR \fIboolean\fR
+.RS 4
+Number the sequence at the beginning and the end of each line\&. Default value: Y
+.RE
+.PP
+\fB\-width\fR \fIinteger\fR
+.RS 4
+Number of nucleotides displayed on each line Default value: 60
+.RE
+.PP
+\fB\-length\fR \fIinteger\fR
+.RS 4
+.RE
+.PP
+\fB\-margin\fR \fIinteger\fR
+.RS 4
+Default value: 10
+.RE
+.PP
+\fB\-name\fR \fIboolean\fR
+.RS 4
+Set this to be false if you do not wish to display the ID name of the sequence\&. Default value: Y
+.RE
+.PP
+\fB\-description\fR \fIboolean\fR
+.RS 4
+Set this to be false if you do not wish to display the description of the sequence\&. Default value: Y
+.RE
+.PP
+\fB\-offset\fR \fIinteger\fR
+.RS 4
+Number from which you want the DNA sequence to be numbered\&. Default value: 1
+.RE
+.PP
+\fB\-html\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+sixpack is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/profit.1e
+++ emboss-6.4.0/debian/manpages/profit.1e
@@ -0,0 +1,74 @@
+'\" t
+.\"     Title: PROFIT
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "PROFIT" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+profit \- Scan one or more sequences with a simple frequency matrix
+.SH "SYNOPSIS"
+.HP \w'\fBprofit\fR\ 'u
+\fBprofit\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBprofit\fR\ 'u
+\fBprofit\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBprofit\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Profiles,Protein:Profiles" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-infile\fR \fIinfile\fR
+.RS 4
+.RE
+.PP
+\fB\-sequence\fR \fIseqall\fR
+.RS 4
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+profit is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/chips.1e
+++ emboss-6.4.0/debian/manpages/chips.1e
@@ -0,0 +1,76 @@
+'\" t
+.\"     Title: CHIPS
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "CHIPS" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+chips \- Calculates Nc codon usage statistic
+.SH "SYNOPSIS"
+.HP \w'\fBchips\fR\ 'u
+\fBchips\fR \fB\-seqall\ \fR\fB\fIseqall\fR\fR \fB\-sum\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBchips\fR\ 'u
+\fBchips\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBchips\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Codon usage" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-seqall\fR \fIseqall\fR
+.RS 4
+.RE
+.SS "Advanced section"
+.PP
+\fB\-sum\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+chips is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/seqretall.1e
+++ emboss-6.4.0/debian/manpages/seqretall.1e
@@ -0,0 +1,70 @@
+'\" t
+.\"     Title: SEQRETALL
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "SEQRETALL" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+seqretall \- Reads and writes (returns) a set of sequences one at a time
+.SH "SYNOPSIS"
+.HP \w'\fBseqretall\fR\ 'u
+\fBseqretall\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR
+.HP \w'\fBseqretall\fR\ 'u
+\fBseqretall\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBseqretall\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqall\fR
+.RS 4
+.RE
+.SS "Output section"
+.PP
+\fB\-outseq\fR \fIseqoutall\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+seqretall is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/mwfilter.1e
+++ emboss-6.4.0/debian/manpages/mwfilter.1e
@@ -0,0 +1,87 @@
+'\" t
+.\"     Title: MWFILTER
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "MWFILTER" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+mwfilter \- Filter noisy data from molecular weights file
+.SH "SYNOPSIS"
+.HP \w'\fBmwfilter\fR\ 'u
+\fBmwfilter\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR \fB\-datafile\ \fR\fB\fIdatafile\fR\fR \fB\-tolerance\ \fR\fB\fIfloat\fR\fR [\fB\-showdel\ \fR\fB\fIboolean\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBmwfilter\fR\ 'u
+\fBmwfilter\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBmwfilter\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Protein:Composition" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-infile\fR \fIinfile\fR
+.RS 4
+.RE
+.PP
+\fB\-datafile\fR \fIdatafile\fR
+.RS 4
+Default value: Emwfilter\&.dat
+.RE
+.SS "Required section"
+.PP
+\fB\-tolerance\fR \fIfloat\fR
+.RS 4
+Default value: 50\&.0
+.RE
+.SS "Additional section"
+.PP
+\fB\-showdel\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+mwfilter is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/dbifasta.1e
+++ emboss-6.4.0/debian/manpages/dbifasta.1e
@@ -0,0 +1,130 @@
+'\" t
+.\"     Title: DBIFASTA
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "DBIFASTA" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+dbifasta \- Index a fasta file database
+.SH "SYNOPSIS"
+.HP \w'\fBdbifasta\fR\ 'u
+\fBdbifasta\fR \fB\-dbname\ \fR\fB\fIstring\fR\fR \fB\-idformat\ \fR\fB\fIlist\fR\fR \fB\-directory\ \fR\fB\fIdirectory\fR\fR \fB\-filenames\ \fR\fB\fIstring\fR\fR \fB\-release\ \fR\fB\fIstring\fR\fR \fB\-date\ \fR\fB\fIstring\fR\fR \fB\-fields\ \fR\fB\fIlist\fR\fR \fB\-exclude\ \fR\fB\fIstring\fR\fR \fB\-maxindex\ \fR\fB\fIinteger\fR\fR \fB\-sortoptions\ \fR\fB\fIstring\fR\fR \fB\-systemsort\ \fR\fB\fIboolean\fR\fR \fB\-cleanup\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR \fB\-indexoutdir\ \fR\fB\fIoutdir\fR\fR
+.HP \w'\fBdbifasta\fR\ 'u
+\fBdbifasta\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBdbifasta\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Database indexing" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-dbname\fR \fIstring\fR
+.RS 4
+.RE
+.PP
+\fB\-idformat\fR \fIlist\fR
+.RS 4
+Default value: idacc
+.RE
+.PP
+\fB\-directory\fR \fIdirectory\fR
+.RS 4
+Default value: \&.
+.RE
+.PP
+\fB\-filenames\fR \fIstring\fR
+.RS 4
+Default value: *\&.dat
+.RE
+.SS "Required section"
+.PP
+\fB\-release\fR \fIstring\fR
+.RS 4
+Default value: 0\&.0
+.RE
+.PP
+\fB\-date\fR \fIstring\fR
+.RS 4
+Default value: 00/00/00
+.RE
+.SS "Advanced section"
+.PP
+\fB\-fields\fR \fIlist\fR
+.RS 4
+Default value: acc
+.RE
+.PP
+\fB\-exclude\fR \fIstring\fR
+.RS 4
+.RE
+.PP
+\fB\-maxindex\fR \fIinteger\fR
+.RS 4
+.RE
+.PP
+\fB\-sortoptions\fR \fIstring\fR
+.RS 4
+Sort options, typically \*(Aq\-T \&.\*(Aq to use current directory for work files and \*(Aq\-k 1,1\*(Aq to force GNU sort to use the first field Default value: \-T \&. \-k 1,1
+.RE
+.PP
+\fB\-systemsort\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-cleanup\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.PP
+\fB\-indexoutdir\fR \fIoutdir\fR
+.RS 4
+Default value: \&.
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+dbifasta is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/goname.1e
+++ emboss-6.4.0/debian/manpages/goname.1e
@@ -0,0 +1,87 @@
+'\" t
+.\"     Title: GONAME
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "GONAME" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+goname \- Find GO ontology terms by name
+.SH "SYNOPSIS"
+.HP \w'\fBgoname\fR\ 'u
+\fBgoname\fR \fB\-query\ \fR\fB\fIstring\fR\fR [\fB\-namespace\ \fR\fB\fIlist\fR\fR] \fB\-subclasses\ \fR\fB\fIboolean\fR\fR \fB\-obsolete\ \fR\fB\fIboolean\fR\fR \fB\-goname\ \fR\fB\fIoutobo\fR\fR
+.HP \w'\fBgoname\fR\ 'u
+\fBgoname\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBgoname\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Ontology:GO,Data retrieval:Ontology data" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-query\fR \fIstring\fR
+.RS 4
+.RE
+.SS "Additional section"
+.PP
+\fB\-namespace\fR \fIlist\fR
+.RS 4
+By default all terms are returned\&. Searches can be limited to one or a few namespaces\&. Default value: *
+.RE
+.SS "Advanced section"
+.PP
+\fB\-subclasses\fR \fIboolean\fR
+.RS 4
+Extend the query matches to include all terms which are specialisations (GO sub\-classes) of the matched type\&. Default value: N
+.RE
+.PP
+\fB\-obsolete\fR \fIboolean\fR
+.RS 4
+The default behaviour is to not use or return obsolete terms\&. This option if set will include all terms\&. Default value: N
+.RE
+.SS "Output section"
+.PP
+\fB\-goname\fR \fIoutobo\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+goname is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/wossname.1e
+++ emboss-6.4.0/debian/manpages/wossname.1e
@@ -0,0 +1,130 @@
+'\" t
+.\"     Title: WOSSNAME
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "WOSSNAME" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+wossname \- Finds programs by keywords in their short description
+.SH "SYNOPSIS"
+.HP \w'\fBwossname\fR\ 'u
+\fBwossname\fR \fB\-search\ \fR\fB\fIstring\fR\fR [\fB\-explode\ \fR\fB\fIboolean\fR\fR] [\fB\-allmatch\ \fR\fB\fIboolean\fR\fR] [\fB\-showkeywords\ \fR\fB\fIboolean\fR\fR] \fB\-emboss\ \fR\fB\fIboolean\fR\fR \fB\-embassy\ \fR\fB\fIboolean\fR\fR \fB\-showembassy\ \fR\fB\fIstring\fR\fR \fB\-colon\ \fR\fB\fIboolean\fR\fR \fB\-gui\ \fR\fB\fIboolean\fR\fR [\fB\-outfile\ \fR\fB\fIoutfile\fR\fR] [\fB\-html\ \fR\fB\fItoggle\fR\fR] [\fB\-groups\ \fR\fB\fIboolean\fR\fR] [\fB\-alphabetic\ \fR\fB\fIboolean\fR\fR]
+.HP \w'\fBwossname\fR\ 'u
+\fBwossname\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBwossname\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Documentation" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-search\fR \fIstring\fR
+.RS 4
+Enter a word or words here and a case\-independent search for it will be made in the one\-line documentation, group names and keywords of all of the EMBOSS programs\&. If no keyword is specified, all programs will be listed\&.
+.RE
+.SS "Additional section"
+.PP
+\fB\-explode\fR \fIboolean\fR
+.RS 4
+The groups that EMBOSS applications belong to have two forms, exploded and not exploded\&. The exploded group names are more numerous and often vaguely phrased than the non\-exploded ones\&. The exploded names are formed from definitions of the group names that start like NAME1:NAME2 and which are then expanded into many combinations of the names as: \*(AqNAME1\*(Aq, \*(AqNAME2\*(Aq, \*(AqNAME1 NAME2\*(Aq, NAME2 NAME1\*(Aq\&. The non\-expanded names are simply like: \*(AqNAME1 NAME2\*(Aq\&. Default value: N
+.RE
+.PP
+\fB\-allmatch\fR \fIboolean\fR
+.RS 4
+By default, all words in the search string must match\&. This option searches for a match to any word in a list of possibilities Default value: Y
+.RE
+.PP
+\fB\-showkeywords\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.SS "Advanced section"
+.PP
+\fB\-emboss\fR \fIboolean\fR
+.RS 4
+If you use this option then EMBOSS program documentation will be searched\&. If this option is set to be false, then only the EMBASSY programs will be searched (if the \-embassy option is true)\&. EMBASSY programs are not strictly part of EMBOSS, but use the same code libraries and share the same look and feel, but are generally developed by people who wish the programs to be outside of the GNU Public Licence scheme Default value: Y
+.RE
+.PP
+\fB\-embassy\fR \fIboolean\fR
+.RS 4
+If you use this option then EMBASSY program documentation will be searched\&. If this option is set to be false, then only the EMBOSS programs will be searched (if the \-emboss option is true)\&. EMBASSY programs are not strictly part of EMBOSS, but use the same code libraries and share the same look and feel, but are generally developed by people who wish the programs to be outside of the GNU Public Licence scheme Default value: Y
+.RE
+.PP
+\fB\-showembassy\fR \fIstring\fR
+.RS 4
+If you use this option then this EMBASSY package program documentation will be searched\&. EMBASSY programs are not strictly part of EMBOSS, but use the same code libraries and share the same look and feel, but are generally developed by people who wish the programs to be outside of the GNU Public Licence scheme
+.RE
+.PP
+\fB\-colon\fR \fIboolean\fR
+.RS 4
+The groups that EMBOSS applications belong to up to two levels, for example the primary group \*(AqALIGNMENT\*(Aq has several sub\-groups, or second\-level groups, e\&.g\&.: CONSENSUS, DIFFERENCES, DOT PLOTS, GLOBAL, LOCAL, MULTIPLE\&. To aid programs that parse the output of wossname that require the names of these subgroups, a colon \*(Aq:\*(Aq will be placed between the first and second level of the group name if this option is true\&. Note: This does not apply if the group names have been exploded with the \*(Aqexplode\*(Aq option\&. Default value: N
+.RE
+.PP
+\fB\-gui\fR \fIboolean\fR
+.RS 4
+This option is intended to help those who are designing Graphical User Interfaces to the EMBOSS applications\&. Some EMBOSS programs are inappropriate for running in a GUI, these include other menu programs and interactive editors\&. This option allows you to only report those programs that can be run from a GUI Default value: N
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+Default value: stdout
+.RE
+.SS "Html section"
+.PP
+\fB\-html\fR \fItoggle\fR
+.RS 4
+If you are sending the output to a file, this will format it for displaying as a table in a WWW document\&. Default value: N
+.RE
+.PP
+\fB\-groups\fR \fIboolean\fR
+.RS 4
+If you use this option, then only the group names will be output to the file Default value: N
+.RE
+.PP
+\fB\-alphabetic\fR \fIboolean\fR
+.RS 4
+If you use this option, then you will get a single list of the program names and descriptions instead of the programs being listed in their functional groups\&. Default value: N
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+wossname is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/maskambignuc.1e
+++ emboss-6.4.0/debian/manpages/maskambignuc.1e
@@ -0,0 +1,75 @@
+'\" t
+.\"     Title: MASKAMBIGNUC
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "MASKAMBIGNUC" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+maskambignuc \- Masks all ambiguity characters in nucleotide sequences with N
+.SH "SYNOPSIS"
+.HP \w'\fBmaskambignuc\fR\ 'u
+\fBmaskambignuc\fR \fB\-feature\ \fR\fB\fIboolean\fR\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR
+.HP \w'\fBmaskambignuc\fR\ 'u
+\fBmaskambignuc\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBmaskambignuc\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-feature\fR \fIboolean\fR
+.RS 4
+.RE
+.PP
+\fB\-sequence\fR \fIseqall\fR
+.RS 4
+.RE
+.SS "Advanced section"
+.SS "Output section"
+.PP
+\fB\-outseq\fR \fIseqoutall\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+maskambignuc is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/pepdigest.1e
+++ emboss-6.4.0/debian/manpages/pepdigest.1e
@@ -0,0 +1,112 @@
+'\" t
+.\"     Title: PEPDIGEST
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "PEPDIGEST" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+pepdigest \- Reports on protein proteolytic enzyme or reagent cleavage sites
+.SH "SYNOPSIS"
+.HP \w'\fBpepdigest\fR\ 'u
+\fBpepdigest\fR \fB\-seqall\ \fR\fB\fIseqall\fR\fR \fB\-mwdata\ \fR\fB\fIdatafile\fR\fR \fB\-menu\ \fR\fB\fIlist\fR\fR \fB\-mono\ \fR\fB\fIboolean\fR\fR \fB\-unfavoured\ \fR\fB\fIboolean\fR\fR \fB\-ragging\ \fR\fB\fIboolean\fR\fR \fB\-termini\ \fR\fB\fIlist\fR\fR \fB\-overlap\ \fR\fB\fIboolean\fR\fR \fB\-allpartials\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIreport\fR\fR
+.HP \w'\fBpepdigest\fR\ 'u
+\fBpepdigest\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBpepdigest\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Protein:Composition" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-seqall\fR \fIseqall\fR
+.RS 4
+.RE
+.PP
+\fB\-mwdata\fR \fIdatafile\fR
+.RS 4
+Molecular weight data for amino acids Default value: Emolwt\&.dat
+.RE
+.SS "Required section"
+.PP
+\fB\-menu\fR \fIlist\fR
+.RS 4
+Default value: 1
+.RE
+.PP
+\fB\-mono\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.SS "Advanced section"
+.PP
+\fB\-unfavoured\fR \fIboolean\fR
+.RS 4
+Trypsin will not normally cut after \*(AqKR\*(Aq if they are followed by any of \*(AqKRIFLP\*(Aq\&. Lys\-C will not normally cut after \*(AqK\*(Aq if it is followed by \*(AqP\*(Aq\&. Arg\-C will not normally cut after \*(AqR\*(Aq if it is followed by \*(AqP\*(Aq\&. V8\-bicarb will not normally cut after \*(AqE\*(Aq if it is followed by any of \*(AqKREP\*(Aq\&. V8\-phosph will not normally cut after \*(AqDE\*(Aq if they are followed by \*(AqP\*(Aq\&. Chymotrypsin will not normally cut after \*(AqFYWLM\*(Aq if they are followed by \*(AqP\*(Aq\&. Specifying unfavoured shows these unfavoured cuts as well as the favoured ones\&.
+.RE
+.PP
+\fB\-ragging\fR \fIboolean\fR
+.RS 4
+Allows semi\-specific and non\-specific digestion\&. This option is particularly useful for generating lists of peptide sequences for protein identification using mass\-spectrometry\&.
+.RE
+.PP
+\fB\-termini\fR \fIlist\fR
+.RS 4
+Default value: 1
+.RE
+.SS "Output section"
+.PP
+\fB\-overlap\fR \fIboolean\fR
+.RS 4
+Used for partial digestion\&. Shows all cuts from favoured cut sites plus 1\&.\&.3, 2\&.\&.4, 3\&.\&.5 etc but not (e\&.g\&.) 2\&.\&.5\&. Overlaps are therefore fragments with exactly one potential cut site within it\&.
+.RE
+.PP
+\fB\-allpartials\fR \fIboolean\fR
+.RS 4
+As for overlap but fragments containing more than one potential cut site are included\&.
+.RE
+.PP
+\fB\-outfile\fR \fIreport\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+pepdigest is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/aaindexextract.1e
+++ emboss-6.4.0/debian/manpages/aaindexextract.1e
@@ -0,0 +1,65 @@
+'\" t
+.\"     Title: AAINDEXEXTRACT
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "AAINDEXEXTRACT" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+aaindexextract \- Extract amino acid property data from AAINDEX
+.SH "SYNOPSIS"
+.HP \w'\fBaaindexextract\fR\ 'u
+\fBaaindexextract\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR
+.HP \w'\fBaaindexextract\fR\ 'u
+\fBaaindexextract\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBaaindexextract\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Database creation" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-infile\fR \fIinfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+aaindexextract is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/taxgetspecies.1e
+++ emboss-6.4.0/debian/manpages/taxgetspecies.1e
@@ -0,0 +1,73 @@
+'\" t
+.\"     Title: TAXGETSPECIES
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "TAXGETSPECIES" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+taxgetspecies \- Get all species under taxon(s)
+.SH "SYNOPSIS"
+.HP \w'\fBtaxgetspecies\fR\ 'u
+\fBtaxgetspecies\fR \fB\-taxons\ \fR\fB\fItaxon\fR\fR \fB\-outfile\ \fR\fB\fIouttaxon\fR\fR
+.HP \w'\fBtaxgetspecies\fR\ 'u
+\fBtaxgetspecies\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBtaxgetspecies\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Ontology:Taxonomy" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-taxons\fR \fItaxon\fR
+.RS 4
+.RE
+.SS "Required section"
+.SS "Additional section"
+.SS "Advanced section"
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIouttaxon\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+taxgetspecies is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/newcpgreport.1e
+++ emboss-6.4.0/debian/manpages/newcpgreport.1e
@@ -0,0 +1,96 @@
+'\" t
+.\"     Title: NEWCPGREPORT
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "NEWCPGREPORT" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+newcpgreport \- Identify CpG islands in nucleotide sequence(s)
+.SH "SYNOPSIS"
+.HP \w'\fBnewcpgreport\fR\ 'u
+\fBnewcpgreport\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-window\ \fR\fB\fIinteger\fR\fR \fB\-shift\ \fR\fB\fIinteger\fR\fR \fB\-minlen\ \fR\fB\fIinteger\fR\fR \fB\-minoe\ \fR\fB\fIfloat\fR\fR \fB\-minpc\ \fR\fB\fIfloat\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBnewcpgreport\fR\ 'u
+\fBnewcpgreport\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBnewcpgreport\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:CpG Islands" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqall\fR
+.RS 4
+.RE
+.SS "Required section"
+.PP
+\fB\-window\fR \fIinteger\fR
+.RS 4
+Default value: 100
+.RE
+.PP
+\fB\-shift\fR \fIinteger\fR
+.RS 4
+Default value: 1
+.RE
+.PP
+\fB\-minlen\fR \fIinteger\fR
+.RS 4
+Default value: 200
+.RE
+.PP
+\fB\-minoe\fR \fIfloat\fR
+.RS 4
+Default value: 0\&.6
+.RE
+.PP
+\fB\-minpc\fR \fIfloat\fR
+.RS 4
+Default value: 50\&.
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+newcpgreport is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/biosed.1e
+++ emboss-6.4.0/debian/manpages/biosed.1e
@@ -0,0 +1,91 @@
+'\" t
+.\"     Title: BIOSED
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "BIOSED" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+biosed \- Replace or delete sequence sections
+.SH "SYNOPSIS"
+.HP \w'\fBbiosed\fR\ 'u
+\fBbiosed\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-targetregion\ \fR\fB\fIstring\fR\fR \fB\-delete\ \fR\fB\fItoggle\fR\fR \fB\-replace\ \fR\fB\fIstring\fR\fR [\fB\-position\ \fR\fB\fIinteger\fR\fR] \fB\-outseq\ \fR\fB\fIseqout\fR\fR
+.HP \w'\fBbiosed\fR\ 'u
+\fBbiosed\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBbiosed\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqall\fR
+.RS 4
+.RE
+.SS "Required section"
+.PP
+\fB\-targetregion\fR \fIstring\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-delete\fR \fItoggle\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-replace\fR \fIstring\fR
+.RS 4
+Default value: A
+.RE
+.SS "Additional section"
+.PP
+\fB\-position\fR \fIinteger\fR
+.RS 4
+.RE
+.SS "Output section"
+.PP
+\fB\-outseq\fR \fIseqout\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+biosed is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/diffseq.1e
+++ emboss-6.4.0/debian/manpages/diffseq.1e
@@ -0,0 +1,96 @@
+'\" t
+.\"     Title: DIFFSEQ
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "DIFFSEQ" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+diffseq \- Compare and report features of two similar sequences
+.SH "SYNOPSIS"
+.HP \w'\fBdiffseq\fR\ 'u
+\fBdiffseq\fR \fB\-asequence\ \fR\fB\fIsequence\fR\fR \fB\-bsequence\ \fR\fB\fIsequence\fR\fR \fB\-wordsize\ \fR\fB\fIinteger\fR\fR [\fB\-globaldifferences\ \fR\fB\fIboolean\fR\fR] \fB\-outfile\ \fR\fB\fIreport\fR\fR \fB\-aoutfeat\ \fR\fB\fIfeatout\fR\fR \fB\-boutfeat\ \fR\fB\fIfeatout\fR\fR
+.HP \w'\fBdiffseq\fR\ 'u
+\fBdiffseq\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBdiffseq\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Alignment:Differences" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-asequence\fR \fIsequence\fR
+.RS 4
+.RE
+.PP
+\fB\-bsequence\fR \fIsequence\fR
+.RS 4
+.RE
+.SS "Required section"
+.PP
+\fB\-wordsize\fR \fIinteger\fR
+.RS 4
+The similar regions between the two sequences are found by creating a hash table of \*(Aqwordsize\*(Aqd subsequences\&. 10 is a reasonable default\&. Making this value larger (20?) may speed up the program slightly, but will mean that any two differences within \*(Aqwordsize\*(Aq of each other will be grouped as a single region of difference\&. This value may be made smaller (4?) to improve the resolution of nearby differences, but the program will go much slower\&. Default value: 10
+.RE
+.SS "Additional section"
+.PP
+\fB\-globaldifferences\fR \fIboolean\fR
+.RS 4
+Normally this program will find regions of identity that are the length of the specified word\-size or greater and will then report the regions of difference between these matching regions\&. This works well and is what most people want if they are working with long overlapping nucleic acid sequences\&. You are usually not interested in the non\-overlapping ends of these sequences\&. If you have protein sequences or short RNA sequences however, you will be interested in differences at the very ends \&. It this option is set to be true then the differences at the ends will also be reported\&. Default value: N
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIreport\fR
+.RS 4
+.RE
+.PP
+\fB\-aoutfeat\fR \fIfeatout\fR
+.RS 4
+File for output of first sequence\*(Aqs features Default value: $(asequence\&.name)\&.diffgff
+.RE
+.PP
+\fB\-boutfeat\fR \fIfeatout\fR
+.RS 4
+File for output of second sequence\*(Aqs features Default value: $(bsequence\&.name)\&.diffgff
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+diffseq is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/vectorstrip.1e
+++ emboss-6.4.0/debian/manpages/vectorstrip.1e
@@ -0,0 +1,108 @@
+'\" t
+.\"     Title: VECTORSTRIP
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "VECTORSTRIP" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+vectorstrip \- Removes vectors from the ends of nucleotide sequence(s)
+.SH "SYNOPSIS"
+.HP \w'\fBvectorstrip\fR\ 'u
+\fBvectorstrip\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-readfile\ \fR\fB\fItoggle\fR\fR \fB\-vectorsfile\ \fR\fB\fIinfile\fR\fR \fB\-mismatch\ \fR\fB\fIinteger\fR\fR \fB\-besthits\ \fR\fB\fIboolean\fR\fR \fB\-alinker\ \fR\fB\fIstring\fR\fR \fB\-blinker\ \fR\fB\fIstring\fR\fR [\fB\-allsequences\ \fR\fB\fIboolean\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR
+.HP \w'\fBvectorstrip\fR\ 'u
+\fBvectorstrip\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBvectorstrip\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqall\fR
+.RS 4
+.RE
+.SS "Vector input options"
+.PP
+\fB\-readfile\fR \fItoggle\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-vectorsfile\fR \fIinfile\fR
+.RS 4
+.RE
+.SS "Required section"
+.PP
+\fB\-mismatch\fR \fIinteger\fR
+.RS 4
+Default value: 10
+.RE
+.PP
+\fB\-besthits\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-alinker\fR \fIstring\fR
+.RS 4
+.RE
+.PP
+\fB\-blinker\fR \fIstring\fR
+.RS 4
+.RE
+.SS "Output section"
+.PP
+\fB\-allsequences\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.PP
+\fB\-outseq\fR \fIseqoutall\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+vectorstrip is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/cpgreport.1e
+++ emboss-6.4.0/debian/manpages/cpgreport.1e
@@ -0,0 +1,81 @@
+'\" t
+.\"     Title: CPGREPORT
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "CPGREPORT" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+cpgreport \- Identify and report CpG\-rich regions in nucleotide sequence(s)
+.SH "SYNOPSIS"
+.HP \w'\fBcpgreport\fR\ 'u
+\fBcpgreport\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-score\ \fR\fB\fIinteger\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR \fB\-outfeat\ \fR\fB\fIfeatout\fR\fR
+.HP \w'\fBcpgreport\fR\ 'u
+\fBcpgreport\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBcpgreport\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:CpG Islands" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqall\fR
+.RS 4
+.RE
+.SS "Required section"
+.PP
+\fB\-score\fR \fIinteger\fR
+.RS 4
+This sets the score for each CG sequence found\&. A value of 17 is more sensitive, but 28 has also been used with some success\&. Default value: 17
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.PP
+\fB\-outfeat\fR \fIfeatout\fR
+.RS 4
+File for output features
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+cpgreport is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/seqretallfeat.1e
+++ emboss-6.4.0/debian/manpages/seqretallfeat.1e
@@ -0,0 +1,70 @@
+'\" t
+.\"     Title: SEQRETALLFEAT
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "SEQRETALLFEAT" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+seqretallfeat \- Reads and writes (returns) one or more sequences
+.SH "SYNOPSIS"
+.HP \w'\fBseqretallfeat\fR\ 'u
+\fBseqretallfeat\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR
+.HP \w'\fBseqretallfeat\fR\ 'u
+\fBseqretallfeat\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBseqretallfeat\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Test" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqall\fR
+.RS 4
+.RE
+.SS "Output section"
+.PP
+\fB\-outseq\fR \fIseqoutall\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+seqretallfeat is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/aligncopy.1e
+++ emboss-6.4.0/debian/manpages/aligncopy.1e
@@ -0,0 +1,87 @@
+'\" t
+.\"     Title: ALIGNCOPY
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "ALIGNCOPY" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+aligncopy \- Reads and writes alignments
+.SH "SYNOPSIS"
+.HP \w'\fBaligncopy\fR\ 'u
+\fBaligncopy\fR \fB\-sequences\ \fR\fB\fIseqset\fR\fR [\fB\-name\ \fR\fB\fIstring\fR\fR] [\fB\-comment\ \fR\fB\fIstring\fR\fR] [\fB\-append\ \fR\fB\fIboolean\fR\fR] \fB\-outfile\ \fR\fB\fIalign\fR\fR
+.HP \w'\fBaligncopy\fR\ 'u
+\fBaligncopy\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBaligncopy\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequences\fR \fIseqset\fR
+.RS 4
+File containing a sequence alignment\&.
+.RE
+.SS "Required section"
+.SS "Additional section"
+.PP
+\fB\-name\fR \fIstring\fR
+.RS 4
+.RE
+.PP
+\fB\-comment\fR \fIstring\fR
+.RS 4
+.RE
+.PP
+\fB\-append\fR \fIboolean\fR
+.RS 4
+This allows you to append the name and comments you have given on to the end of the existing alignment header\&. Default value: N
+.RE
+.SS "Advanced section"
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIalign\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+aligncopy is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/cons.1e
+++ emboss-6.4.0/debian/manpages/cons.1e
@@ -0,0 +1,96 @@
+'\" t
+.\"     Title: CONS
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "CONS" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+cons \- Create a consensus sequence from a multiple alignment
+.SH "SYNOPSIS"
+.HP \w'\fBcons\fR\ 'u
+\fBcons\fR \fB\-sequence\ \fR\fB\fIseqset\fR\fR [\fB\-datafile\ \fR\fB\fImatrix\fR\fR] [\fB\-plurality\ \fR\fB\fIfloat\fR\fR] [\fB\-identity\ \fR\fB\fIinteger\fR\fR] [\fB\-setcase\ \fR\fB\fIfloat\fR\fR] \fB\-outseq\ \fR\fB\fIseqout\fR\fR [\fB\-name\ \fR\fB\fIstring\fR\fR]
+.HP \w'\fBcons\fR\ 'u
+\fBcons\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBcons\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Alignment:Consensus" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqset\fR
+.RS 4
+File containing a sequence alignment\&.
+.RE
+.PP
+\fB\-datafile\fR \fImatrix\fR
+.RS 4
+This is the scoring matrix file used when comparing sequences\&. By default it is the file \*(AqEBLOSUM62\*(Aq (for proteins) or the file \*(AqEDNAFULL\*(Aq (for nucleic sequences)\&. These files are found in the \*(Aqdata\*(Aq directory of the EMBOSS installation\&.
+.RE
+.SS "Additional section"
+.PP
+\fB\-plurality\fR \fIfloat\fR
+.RS 4
+Set a cut\-off for the number of positive matches below which there is no consensus\&. The default plurality is taken as half the total weight of all the sequences in the alignment\&. Default value: @( $(sequence\&.totweight) / 2)
+.RE
+.PP
+\fB\-identity\fR \fIinteger\fR
+.RS 4
+Provides the facility of setting the required number of identities at a site for it to give a consensus at that position\&. Therefore, if this is set to the number of sequences in the alignment only columns of identities contribute to the consensus\&.
+.RE
+.PP
+\fB\-setcase\fR \fIfloat\fR
+.RS 4
+Sets the threshold for the positive matches above which the consensus is is upper\-case and below which the consensus is in lower\-case\&. Default value: @( $(sequence\&.totweight) / 2)
+.RE
+.SS "Output section"
+.PP
+\fB\-outseq\fR \fIseqout\fR
+.RS 4
+.RE
+.PP
+\fB\-name\fR \fIstring\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+cons is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/noreturn.1e
+++ emboss-6.4.0/debian/manpages/noreturn.1e
@@ -0,0 +1,76 @@
+'\" t
+.\"     Title: NORETURN
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "NORETURN" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+noreturn \- Remove carriage return from ASCII files
+.SH "SYNOPSIS"
+.HP \w'\fBnoreturn\fR\ 'u
+\fBnoreturn\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR \fB\-system\ \fR\fB\fIlist\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBnoreturn\fR\ 'u
+\fBnoreturn\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBnoreturn\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-infile\fR \fIinfile\fR
+.RS 4
+.RE
+.SS "Advanced section"
+.PP
+\fB\-system\fR \fIlist\fR
+.RS 4
+Default value: unix
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+noreturn is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/degapseq.1e
+++ emboss-6.4.0/debian/manpages/degapseq.1e
@@ -0,0 +1,70 @@
+'\" t
+.\"     Title: DEGAPSEQ
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "DEGAPSEQ" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+degapseq \- Removes non\-alphabetic (e\&.g\&. gap) characters from sequences
+.SH "SYNOPSIS"
+.HP \w'\fBdegapseq\fR\ 'u
+\fBdegapseq\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR
+.HP \w'\fBdegapseq\fR\ 'u
+\fBdegapseq\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBdegapseq\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqall\fR
+.RS 4
+.RE
+.SS "Output section"
+.PP
+\fB\-outseq\fR \fIseqoutall\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+degapseq is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/martseqs.1e
+++ emboss-6.4.0/debian/manpages/martseqs.1e
@@ -0,0 +1,81 @@
+'\" t
+.\"     Title: MARTSEQS
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "MARTSEQS" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+martseqs \- Show Biomart datasets that can return sequences
+.SH "SYNOPSIS"
+.HP \w'\fBmartseqs\fR\ 'u
+\fBmartseqs\fR \fB\-host\ \fR\fB\fIstring\fR\fR \fB\-path\ \fR\fB\fIstring\fR\fR \fB\-port\ \fR\fB\fIinteger\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBmartseqs\fR\ 'u
+\fBmartseqs\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBmartseqs\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-host\fR \fIstring\fR
+.RS 4
+Default value: www\&.biomart\&.org
+.RE
+.PP
+\fB\-path\fR \fIstring\fR
+.RS 4
+Default value: /biomart/martservice
+.RE
+.PP
+\fB\-port\fR \fIinteger\fR
+.RS 4
+Default value: 80
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+martseqs is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/xmltransform.1e
+++ emboss-6.4.0/debian/manpages/xmltransform.1e
@@ -0,0 +1,81 @@
+'\" t
+.\"     Title: XMLTRANSFORM
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "XMLTRANSFORM" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+xmltransform \- Convert an XML document to a different format using a supplied XSLT file
+.SH "SYNOPSIS"
+.HP \w'\fBxmltransform\fR\ 'u
+\fBxmltransform\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR \fB\-xslt\ \fR\fB\fIinfile\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR \fB\-logfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBxmltransform\fR\ 'u
+\fBxmltransform\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBxmltransform\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Misc" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-infile\fR \fIinfile\fR
+.RS 4
+.RE
+.PP
+\fB\-xslt\fR \fIinfile\fR
+.RS 4
+.RE
+.SS "Required section"
+.SS "Additional section"
+.SS "Advanced section"
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.PP
+\fB\-logfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+xmltransform is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/coderet.1e
+++ emboss-6.4.0/debian/manpages/coderet.1e
@@ -0,0 +1,86 @@
+'\" t
+.\"     Title: CODERET
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "CODERET" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+coderet \- Extract CDS, mRNA and translations from feature tables
+.SH "SYNOPSIS"
+.HP \w'\fBcoderet\fR\ 'u
+\fBcoderet\fR \fB\-seqall\ \fR\fB\fIseqall\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR \fB\-cdsoutseq\ \fR\fB\fIseqoutall\fR\fR \fB\-mrnaoutseq\ \fR\fB\fIseqoutall\fR\fR \fB\-translationoutseq\ \fR\fB\fIseqoutall\fR\fR \fB\-restoutseq\ \fR\fB\fIseqoutall\fR\fR
+.HP \w'\fBcoderet\fR\ 'u
+\fBcoderet\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBcoderet\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Translation,Data retrieval:Sequence data" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-seqall\fR \fIseqall\fR
+.RS 4
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.PP
+\fB\-cdsoutseq\fR \fIseqoutall\fR
+.RS 4
+.RE
+.PP
+\fB\-mrnaoutseq\fR \fIseqoutall\fR
+.RS 4
+.RE
+.PP
+\fB\-translationoutseq\fR \fIseqoutall\fR
+.RS 4
+.RE
+.PP
+\fB\-restoutseq\fR \fIseqoutall\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+coderet is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/seqretsetall.1e
+++ emboss-6.4.0/debian/manpages/seqretsetall.1e
@@ -0,0 +1,74 @@
+'\" t
+.\"     Title: SEQRETSETALL
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "SEQRETSETALL" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+seqretsetall \- Reads and writes (returns) many sets of sequences
+.SH "SYNOPSIS"
+.HP \w'\fBseqretsetall\fR\ 'u
+\fBseqretsetall\fR \fB\-feature\ \fR\fB\fIboolean\fR\fR \fB\-sequence\ \fR\fB\fIseqsetall\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR
+.HP \w'\fBseqretsetall\fR\ 'u
+\fBseqretsetall\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBseqretsetall\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-feature\fR \fIboolean\fR
+.RS 4
+.RE
+.PP
+\fB\-sequence\fR \fIseqsetall\fR
+.RS 4
+.RE
+.SS "Output section"
+.PP
+\fB\-outseq\fR \fIseqoutall\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+seqretsetall is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/seqrettype.1e
+++ emboss-6.4.0/debian/manpages/seqrettype.1e
@@ -0,0 +1,84 @@
+'\" t
+.\"     Title: SEQRETTYPE
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "SEQRETTYPE" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+seqrettype \- Reads and writes (returns) sequences
+.SH "SYNOPSIS"
+.HP \w'\fBseqrettype\fR\ 'u
+\fBseqrettype\fR \fB\-feature\ \fR\fB\fIboolean\fR\fR \fB\-type\ \fR\fB\fIlist\fR\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-firstonly\ \fR\fB\fIboolean\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR
+.HP \w'\fBseqrettype\fR\ 'u
+\fBseqrettype\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBseqrettype\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-feature\fR \fIboolean\fR
+.RS 4
+.RE
+.PP
+\fB\-type\fR \fIlist\fR
+.RS 4
+Default value: any
+.RE
+.PP
+\fB\-sequence\fR \fIseqall\fR
+.RS 4
+.RE
+.SS "Advanced section"
+.PP
+\fB\-firstonly\fR \fIboolean\fR
+.RS 4
+.RE
+.SS "Output section"
+.PP
+\fB\-outseq\fR \fIseqoutall\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+seqrettype is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/dbgeturl.1e
+++ emboss-6.4.0/debian/manpages/dbgeturl.1e
@@ -0,0 +1,85 @@
+'\" t
+.\"     Title: DBGETURL
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "DBGETURL" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+dbgeturl \- Retrieve links to database entries for a named database, data type and data identifier
+.SH "SYNOPSIS"
+.HP \w'\fBdbgeturl\fR\ 'u
+\fBdbgeturl\fR \fB\-database\ \fR\fB\fIstring\fR\fR \fB\-datatype\ \fR\fB\fIstring\fR\fR \fB\-identifier\ \fR\fB\fIstring\fR\fR [\fB\-outfile\ \fR\fB\fIoutfile\fR\fR]
+.HP \w'\fBdbgeturl\fR\ 'u
+\fBdbgeturl\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBdbgeturl\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Misc" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-database\fR \fIstring\fR
+.RS 4
+This is the name of a database from the catalogue of public databases in the EMBOSS data file DRCAT\&.dat\&. If you are unsure of the available databases use dbfind\&. If you have a database name but are not sure its valid, use isdbname\&.
+.RE
+.PP
+\fB\-datatype\fR \fIstring\fR
+.RS 4
+This is the name of a retrievable datatype from the catalogue of public databases in the EMBOSS data file DRCAT\&.dat\&. The names are terms from the \*(Aqdata\*(Aq branch of the EDAM ontology, http://edamontology\&.sourceforge\&.net/\&. If you are unsure of the available retrievable datatypes for a given database, use dbtellquery\&. If you have a datatype name but are not sure its valid, use isdbdata\&.
+.RE
+.PP
+\fB\-identifier\fR \fIstring\fR
+.RS 4
+This is a data identifier (e\&.g\&. a sequence accession number) that is used to specify the data (of type \*(Aqdatatype\*(Aq) to retrieve\&. If you\*(Aqre unsure of the data identifier(s) that are used for a given query (database/datatype) use dbtellquery\&. The types of data identifier are listed under the \*(AqData identifier\*(Aq branch of the EDAM ontology (http://edamontology\&.sourceforge\&.net/)\&. For example values, see the catalogue of public databases in the EMBOSS data file DRCAT\&.dat\&. If you have a data identifier but are unsure of its type, use idtell\&.
+.RE
+.SS "Required section"
+.SS "Additional section"
+.SS "Advanced section"
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+Default value: stdout
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+dbgeturl is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/wordcount.1e
+++ emboss-6.4.0/debian/manpages/wordcount.1e
@@ -0,0 +1,82 @@
+'\" t
+.\"     Title: WORDCOUNT
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "WORDCOUNT" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+wordcount \- Count and extract unique words in molecular sequence(s)
+.SH "SYNOPSIS"
+.HP \w'\fBwordcount\fR\ 'u
+\fBwordcount\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-wordsize\ \fR\fB\fIinteger\fR\fR [\fB\-mincount\ \fR\fB\fIinteger\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBwordcount\fR\ 'u
+\fBwordcount\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBwordcount\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Composition,Protein:Composition" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqall\fR
+.RS 4
+.RE
+.SS "Required section"
+.PP
+\fB\-wordsize\fR \fIinteger\fR
+.RS 4
+Default value: @($(acdprotein)? 2 : 4)
+.RE
+.SS "Additional section"
+.PP
+\fB\-mincount\fR \fIinteger\fR
+.RS 4
+Default value: 1
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+wordcount is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/revseq.1e
+++ emboss-6.4.0/debian/manpages/revseq.1e
@@ -0,0 +1,81 @@
+'\" t
+.\"     Title: REVSEQ
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "REVSEQ" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+revseq \- Reverse and complement a nucleotide sequence
+.SH "SYNOPSIS"
+.HP \w'\fBrevseq\fR\ 'u
+\fBrevseq\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-reverse\ \fR\fB\fIboolean\fR\fR \fB\-complement\ \fR\fB\fIboolean\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR
+.HP \w'\fBrevseq\fR\ 'u
+\fBrevseq\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBrevseq\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqall\fR
+.RS 4
+.RE
+.SS "Advanced section"
+.PP
+\fB\-reverse\fR \fIboolean\fR
+.RS 4
+Set this to be false if you do not wish to reverse the output sequence Default value: Y
+.RE
+.PP
+\fB\-complement\fR \fIboolean\fR
+.RS 4
+Set this to be false if you do not wish to complement the output sequence Default value: Y
+.RE
+.SS "Output section"
+.PP
+\fB\-outseq\fR \fIseqoutall\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+revseq is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/showseq.1e
+++ emboss-6.4.0/debian/manpages/showseq.1e
@@ -0,0 +1,273 @@
+'\" t
+.\"     Title: SHOWSEQ
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "SHOWSEQ" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+showseq \- Displays sequences with features in pretty format
+.SH "SYNOPSIS"
+.HP \w'\fBshowseq\fR\ 'u
+\fBshowseq\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-mfile\ \fR\fB\fIdatafile\fR\fR \fB\-format\ \fR\fB\fIlist\fR\fR \fB\-things\ \fR\fB\fIlist\fR\fR [\fB\-translate\ \fR\fB\fIrange\fR\fR] [\fB\-revtranslate\ \fR\fB\fIrange\fR\fR] [\fB\-uppercase\ \fR\fB\fIrange\fR\fR] [\fB\-highlight\ \fR\fB\fIrange\fR\fR] [\fB\-annotation\ \fR\fB\fIrange\fR\fR] [\fB\-enzymes\ \fR\fB\fIstring\fR\fR] [\fB\-table\ \fR\fB\fIlist\fR\fR] [\fB\-sourcematch\ \fR\fB\fIstring\fR\fR] [\fB\-typematch\ \fR\fB\fIstring\fR\fR] [\fB\-sensematch\ \fR\fB\fIinteger\fR\fR] [\fB\-minscore\ \fR\fB\fIfloat\fR\fR] [\fB\-maxscore\ \fR\fB\fIfloat\fR\fR] [\fB\-tagmatch\ \fR\fB\fIstring\fR\fR] [\fB\-valuematch\ \fR\fB\fIstring\fR\fR] [\fB\-stricttags\ \fR\fB\fIboolean\fR\fR] \fB\-flatreformat\ \fR\fB\fIboolean\fR\fR \fB\-mincuts\ \fR\fB\fIinteger\fR\fR \fB\-maxcuts\ \fR\fB\fIinteger\fR\fR \fB\-sitelen\ \fR\fB\fIinteger\fR\fR \fB\-single\ \fR\fB\fIboolean\fR\fR \fB\-blunt\ \fR\fB\fIboolean\fR\fR \fB\-sticky\ \fR\fB\fIboolean\fR\fR \fB\-ambiguity\ \fR\fB\fIboolean\fR\fR \fB\-plasmid\ \fR\fB\fIboolean\fR\fR \fB\-methylation\ \fR\fB\fIboolean\fR\fR \fB\-commercial\ \fR\fB\fIboolean\fR\fR \fB\-limit\ \fR\fB\fIboolean\fR\fR \fB\-orfminsize\ \fR\fB\fIinteger\fR\fR \fB\-threeletter\ \fR\fB\fIboolean\fR\fR \fB\-number\ \fR\fB\fIboolean\fR\fR \fB\-width\ \fR\fB\fIinteger\fR\fR \fB\-length\ \fR\fB\fIinteger\fR\fR \fB\-margin\ \fR\fB\fIinteger\fR\fR \fB\-name\ \fR\fB\fIboolean\fR\fR \fB\-description\ \fR\fB\fIboolean\fR\fR \fB\-offset\ \fR\fB\fIinteger\fR\fR \fB\-html\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBshowseq\fR\ 'u
+\fBshowseq\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBshowseq\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Translation,Nucleic:Restriction" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqall\fR
+.RS 4
+.RE
+.PP
+\fB\-mfile\fR \fIdatafile\fR
+.RS 4
+Default value: Emethylsites\&.dat
+.RE
+.SS "Required section"
+.PP
+\fB\-format\fR \fIlist\fR
+.RS 4
+Default value: 2
+.RE
+.PP
+\fB\-things\fR \fIlist\fR
+.RS 4
+Specify a list of one or more code characters in the order in which you wish things to be displayed one above the other down the page\&. For example if you wish to see things displayed in the order: sequence, complement sequence, ticks line, frame 1 translation, blank line; then you should enter \*(AqS,C,T,1,B\*(Aq\&. Default value: B,N,T,S,A,F
+.RE
+.SS "Additional section"
+.PP
+\fB\-translate\fR \fIrange\fR
+.RS 4
+Regions to translate (if translating)\&. If this is left blank the complete sequence is translated\&. A set of regions is specified by a set of pairs of positions\&. The positions are integers\&. They are separated by any non\-digit, non\-alpha character\&. Examples of region specifications are: 24\-45, 56\-78 1:45, 67=99;765\&.\&.888
+.RE
+.PP
+\fB\-revtranslate\fR \fIrange\fR
+.RS 4
+Regions to translate (if translating)\&. If this is left blank the complete sequence is translated\&. A set of regions is specified by a set of pairs of positions\&. The positions are integers\&. They are separated by any non\-digit, non\-alpha character\&. Examples of region specifications are: 78\-56, 45\-24, 888\&.\&.765, 99=67; 45:1
+.RE
+.PP
+\fB\-uppercase\fR \fIrange\fR
+.RS 4
+Regions to put in uppercase\&. If this is left blank, then the sequence case is left alone\&. A set of regions is specified by a set of pairs of positions\&. The positions are integers\&. They are separated by any non\-digit, non\-alpha character\&. Examples of region specifications are: 24\-45, 56\-78 1:45, 67=99;765\&.\&.888 1,5,8,10,23,45,57,99
+.RE
+.PP
+\fB\-highlight\fR \fIrange\fR
+.RS 4
+Regions to colour if formatting for HTML\&. If this is left blank, then the sequence is left alone\&. A set of regions is specified by a set of pairs of positions\&. The positions are integers\&. They are followed by any valid HTML font colour\&. Examples of region specifications are: 24\-45 blue 56\-78 orange 1\-100 green 120\-156 red A file of ranges to colour (one range per line) can be specified as \*(Aq@filename\*(Aq\&.
+.RE
+.PP
+\fB\-annotation\fR \fIrange\fR
+.RS 4
+Regions to annotate by marking\&. If this is left blank, then no annotation is added\&. A set of regions is specified by a set of pairs of positions followed by optional text\&. The positions are integers\&. They are followed by any text (but not digits when on the command\-line)\&. Examples of region specifications are: 24\-45 new domain 56\-78 match to Mouse 1\-100 First part 120\-156 oligo A file of ranges to annotate (one range per line) can be specified as \*(Aq@filename\*(Aq\&.
+.RE
+.PP
+\fB\-enzymes\fR \fIstring\fR
+.RS 4
+The name \*(Aqall\*(Aq reads in all enzyme names from the REBASE database\&. You can specify enzymes by giving their names with commas between then, such as: \*(AqHincII,hinfI,ppiI,hindiii\*(Aq\&. The case of the names is not important\&. You can specify a file of enzyme names to read in by giving the name of the file holding the enzyme names with a \*(Aq@\*(Aq character in front of it, for example, \*(Aq@enz\&.list\*(Aq\&. Blank lines and lines starting with a hash character or \*(Aq!\*(Aq are ignored and all other lines are concatenated together with a comma character \*(Aq,\*(Aq and then treated as the list of enzymes to search for\&. An example of a file of enzyme names is: ! my enzymes HincII, ppiII ! other enzymes hindiii HinfI PpiI Default value: all
+.RE
+.PP
+\fB\-table\fR \fIlist\fR
+.RS 4
+.RE
+.SS "Feature display options"
+.PP
+\fB\-sourcematch\fR \fIstring\fR
+.RS 4
+By default any feature source in the feature table is shown\&. You can set this to match any feature source you wish to show\&. The source name is usually either the name of the program that detected the feature or it is the feature table (eg: EMBL) that the feature came from\&. The source may be wildcarded by using \*(Aq*\*(Aq\&. If you wish to show more than one source, separate their names with the character \*(Aq|\*(Aq, eg: gene* | embl Default value: *
+.RE
+.PP
+\fB\-typematch\fR \fIstring\fR
+.RS 4
+By default any feature type in the feature table is shown\&. You can set this to match any feature type you wish to show\&. See http://www\&.ebi\&.ac\&.uk/embl/WebFeat/ for a list of the EMBL feature types and see Appendix A of the Swissprot user manual in http://www\&.expasy\&.org/sprot/userman\&.html for a list of the Swissprot feature types\&. The type may be wildcarded by using \*(Aq*\*(Aq\&. If you wish to show more than one type, separate their names with the character \*(Aq|\*(Aq, eg: *UTR | intron Default value: *
+.RE
+.PP
+\fB\-sensematch\fR \fIinteger\fR
+.RS 4
+By default any feature type in the feature table is shown\&. You can set this to match any feature sense you wish to show\&. 0 \- any sense, 1 \- forward sense, \-1 \- reverse sense
+.RE
+.PP
+\fB\-minscore\fR \fIfloat\fR
+.RS 4
+Minimum score of feature to display (see also maxscore) Default value: 0\&.0
+.RE
+.PP
+\fB\-maxscore\fR \fIfloat\fR
+.RS 4
+Maximum score of feature to display\&. If both minscore and maxscore are zero (the default), then any score is ignored Default value: 0\&.0
+.RE
+.PP
+\fB\-tagmatch\fR \fIstring\fR
+.RS 4
+Tags are the types of extra values that a feature may have\&. For example in the EMBL feature table, a \*(AqCDS\*(Aq type of feature may have the tags \*(Aq/codon\*(Aq, \*(Aq/codon_start\*(Aq, \*(Aq/db_xref\*(Aq, \*(Aq/EC_number\*(Aq, \*(Aq/evidence\*(Aq, \*(Aq/exception\*(Aq, \*(Aq/function\*(Aq, \*(Aq/gene\*(Aq, \*(Aq/label\*(Aq, \*(Aq/map\*(Aq, \*(Aq/note\*(Aq, \*(Aq/number\*(Aq, \*(Aq/partial\*(Aq, \*(Aq/product\*(Aq, \*(Aq/protein_id\*(Aq, \*(Aq/pseudo\*(Aq, \*(Aq/standard_name\*(Aq, \*(Aq/translation\*(Aq, \*(Aq/transl_except\*(Aq, \*(Aq/transl_table\*(Aq, or \*(Aq/usedin\*(Aq\&. Some of these tags also have values, for example \*(Aq/gene\*(Aq can have the value of the gene name\&. By default any feature tag in the feature table is shown\&. You can set this to match any feature tag you wish to show\&. The tag may be wildcarded by using \*(Aq*\*(Aq\&. If you wish to show more than one tag, separate their names with the character \*(Aq|\*(Aq, eg: gene | label Default value: *
+.RE
+.PP
+\fB\-valuematch\fR \fIstring\fR
+.RS 4
+Tag values are the values associated with a feature tag\&. Tags are the types of extra values that a feature may have\&. For example in the EMBL feature table, a \*(AqCDS\*(Aq type of feature may have the tags \*(Aq/codon\*(Aq, \*(Aq/codon_start\*(Aq, \*(Aq/db_xref\*(Aq, \*(Aq/EC_number\*(Aq, \*(Aq/evidence\*(Aq, \*(Aq/exception\*(Aq, \*(Aq/function\*(Aq, \*(Aq/gene\*(Aq, \*(Aq/label\*(Aq, \*(Aq/map\*(Aq, \*(Aq/note\*(Aq, \*(Aq/number\*(Aq, \*(Aq/partial\*(Aq, \*(Aq/product\*(Aq, \*(Aq/protein_id\*(Aq, \*(Aq/pseudo\*(Aq, \*(Aq/standard_name\*(Aq, \*(Aq/translation\*(Aq, \*(Aq/transl_except\*(Aq, \*(Aq/transl_table\*(Aq, or \*(Aq/usedin\*(Aq\&. Only some of these tags can have values, for example \*(Aq/gene\*(Aq can have the value of the gene name\&. By default any feature tag value in the feature table is shown\&. You can set this to match any feature tag value you wish to show\&. The tag value may be wildcarded by using \*(Aq*\*(Aq\&. If you wish to show more than one tag value, separate their names with the character \*(Aq|\*(Aq, eg: pax* | 10 Default value: *
+.RE
+.PP
+\fB\-stricttags\fR \fIboolean\fR
+.RS 4
+By default if any tag/value pair in a feature matches the specified tag and value, then all the tags/value pairs of that feature will be displayed\&. If this is set to be true, then only those tag/value pairs in a feature that match the specified tag and value will be displayed\&. Default value: N
+.RE
+.SS "Advanced section"
+.SS "Restriction map options"
+.PP
+\fB\-flatreformat\fR \fIboolean\fR
+.RS 4
+This changes the output format to one where the recognition site is indicated by a row of \*(Aq===\*(Aq characters and the cut site is pointed to by a \*(Aq>\*(Aq character in the forward sense, or a \*(Aq<\*(Aq in the reverse sense strand\&. Default value: N
+.RE
+.PP
+\fB\-mincuts\fR \fIinteger\fR
+.RS 4
+This sets the minimum number of cuts for any restriction enzyme that will be considered\&. Any enzymes that cut fewer times than this will be ignored\&. Default value: 1
+.RE
+.PP
+\fB\-maxcuts\fR \fIinteger\fR
+.RS 4
+This sets the maximum number of cuts for any restriction enzyme that will be considered\&. Any enzymes that cut more times than this will be ignored\&. Default value: 2000000000
+.RE
+.PP
+\fB\-sitelen\fR \fIinteger\fR
+.RS 4
+This sets the minimum length of the restriction enzyme recognition site\&. Any enzymes with sites shorter than this will be ignored\&. Default value: 4
+.RE
+.PP
+\fB\-single\fR \fIboolean\fR
+.RS 4
+If this is set then this forces the values of the mincuts and maxcuts qualifiers to both be 1\&. Any other value you may have set them to will be ignored\&. Default value: N
+.RE
+.PP
+\fB\-blunt\fR \fIboolean\fR
+.RS 4
+This allows those enzymes which cut at the same position on the forward and reverse strands to be considered\&. Default value: Y
+.RE
+.PP
+\fB\-sticky\fR \fIboolean\fR
+.RS 4
+This allows those enzymes which cut at different positions on the forward and reverse strands, leaving an overhang, to be considered\&. Default value: Y
+.RE
+.PP
+\fB\-ambiguity\fR \fIboolean\fR
+.RS 4
+This allows those enzymes which have one or more \*(AqN\*(Aq ambiguity codes in their pattern to be considered Default value: Y
+.RE
+.PP
+\fB\-plasmid\fR \fIboolean\fR
+.RS 4
+If this is set then this allows searches for restriction enzyme recognition site and cut positions that span the end of the sequence to be considered\&. Default value: N
+.RE
+.PP
+\fB\-methylation\fR \fIboolean\fR
+.RS 4
+If this is set then RE recognition sites will not match methylated bases\&. Default value: N
+.RE
+.PP
+\fB\-commercial\fR \fIboolean\fR
+.RS 4
+If this is set, then only those enzymes with a commercial supplier will be searched for\&. This qualifier is ignored if you have specified an explicit list of enzymes to search for, rather than searching through \*(Aqall\*(Aq the enzymes in the REBASE database\&. It is assumed that, if you are asking for an explicit enzyme, then you probably know where to get it from and so all enzymes names that you have asked to be searched for, and which cut, will be reported whether or not they have a commercial supplier\&. Default value: Y
+.RE
+.PP
+\fB\-limit\fR \fIboolean\fR
+.RS 4
+This limits the reporting of enzymes to just one enzyme from each group of isoschizomers\&. The enzyme chosen to represent an isoschizomer group is the prototype indicated in the data file \*(Aqembossre\&.equ\*(Aq, which is created by the program \*(Aqrebaseextract\*(Aq\&. If you prefer different prototypes to be used, make a copy of embossre\&.equ in your home directory and edit it\&. If this value is set to be false then all of the input enzymes will be reported\&. You might like to set this to false if you are supplying an explicit set of enzymes rather than searching \*(Aqall\*(Aq of them\&. Default value: Y
+.RE
+.PP
+\fB\-orfminsize\fR \fIinteger\fR
+.RS 4
+This sets the minimum size of Open Reading Frames (ORFs) to display in the translations\&. All other translation regions are masked by changing the amino acids to \*(Aq\-\*(Aq characters\&.
+.RE
+.PP
+\fB\-threeletter\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-number\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-width\fR \fIinteger\fR
+.RS 4
+Default value: 60
+.RE
+.PP
+\fB\-length\fR \fIinteger\fR
+.RS 4
+.RE
+.PP
+\fB\-margin\fR \fIinteger\fR
+.RS 4
+Default value: 10
+.RE
+.PP
+\fB\-name\fR \fIboolean\fR
+.RS 4
+Set this to be false if you do not wish to display the ID name of the sequence Default value: Y
+.RE
+.PP
+\fB\-description\fR \fIboolean\fR
+.RS 4
+Set this to be false if you do not wish to display the description of the sequence Default value: Y
+.RE
+.PP
+\fB\-offset\fR \fIinteger\fR
+.RS 4
+Default value: 1
+.RE
+.PP
+\fB\-html\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+showseq is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/sigcleave.1e
+++ emboss-6.4.0/debian/manpages/sigcleave.1e
@@ -0,0 +1,82 @@
+'\" t
+.\"     Title: SIGCLEAVE
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "SIGCLEAVE" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+sigcleave \- Reports on signal cleavage sites in a protein sequence
+.SH "SYNOPSIS"
+.HP \w'\fBsigcleave\fR\ 'u
+\fBsigcleave\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-minweight\ \fR\fB\fIfloat\fR\fR [\fB\-prokaryote\ \fR\fB\fIboolean\fR\fR] \fB\-outfile\ \fR\fB\fIreport\fR\fR
+.HP \w'\fBsigcleave\fR\ 'u
+\fBsigcleave\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBsigcleave\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Protein:Functional sites,Protein:Motifs" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqall\fR
+.RS 4
+.RE
+.SS "Required section"
+.PP
+\fB\-minweight\fR \fIfloat\fR
+.RS 4
+Minimum scoring weight value for the predicted cleavage site Default value: 3\&.5
+.RE
+.SS "Additional section"
+.PP
+\fB\-prokaryote\fR \fIboolean\fR
+.RS 4
+Specifies the sequence is prokaryotic and changes the default scoring data file name
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIreport\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+sigcleave is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/ontogetroot.1e
+++ emboss-6.4.0/debian/manpages/ontogetroot.1e
@@ -0,0 +1,77 @@
+'\" t
+.\"     Title: ONTOGETROOT
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "ONTOGETROOT" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+ontogetroot \- Get ontology root terms by child identifier
+.SH "SYNOPSIS"
+.HP \w'\fBontogetroot\fR\ 'u
+\fBontogetroot\fR \fB\-oboterms\ \fR\fB\fIobo\fR\fR [\fB\-obsolete\ \fR\fB\fIboolean\fR\fR] \fB\-outfile\ \fR\fB\fIoutobo\fR\fR
+.HP \w'\fBontogetroot\fR\ 'u
+\fBontogetroot\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBontogetroot\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Ontology,Data retrieval:Ontology data" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-oboterms\fR \fIobo\fR
+.RS 4
+.RE
+.SS "Additional section"
+.PP
+\fB\-obsolete\fR \fIboolean\fR
+.RS 4
+The default behaviour is to not use or return obsolete terms\&. This option if set will include all terms\&. Default value: N
+.RE
+.SS "Advanced section"
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutobo\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+ontogetroot is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/wobble.1e
+++ emboss-6.4.0/debian/manpages/wobble.1e
@@ -0,0 +1,86 @@
+'\" t
+.\"     Title: WOBBLE
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "WOBBLE" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+wobble \- Plot third base position variability in a nucleotide sequence
+.SH "SYNOPSIS"
+.HP \w'\fBwobble\fR\ 'u
+\fBwobble\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR [\fB\-window\ \fR\fB\fIinteger\fR\fR] \fB\-bases\ \fR\fB\fIstring\fR\fR \fB\-graph\ \fR\fB\fIxygraph\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBwobble\fR\ 'u
+\fBwobble\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBwobble\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Gene finding" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIsequence\fR
+.RS 4
+.RE
+.SS "Additional section"
+.PP
+\fB\-window\fR \fIinteger\fR
+.RS 4
+Default value: 30
+.RE
+.SS "Advanced section"
+.PP
+\fB\-bases\fR \fIstring\fR
+.RS 4
+Default value: GC
+.RE
+.SS "Output section"
+.PP
+\fB\-graph\fR \fIxygraph\fR
+.RS 4
+.RE
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+wobble is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/codcopy.1e
+++ emboss-6.4.0/debian/manpages/codcopy.1e
@@ -0,0 +1,71 @@
+'\" t
+.\"     Title: CODCOPY
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "CODCOPY" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+codcopy \- Copy and reformat a codon usage table
+.SH "SYNOPSIS"
+.HP \w'\fBcodcopy\fR\ 'u
+\fBcodcopy\fR \fB\-infile\ \fR\fB\fIcodon\fR\fR \fB\-outfile\ \fR\fB\fIoutcodon\fR\fR
+.HP \w'\fBcodcopy\fR\ 'u
+\fBcodcopy\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBcodcopy\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Data retrieval,Nucleic:Codon usage,Edit" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-infile\fR \fIcodon\fR
+.RS 4
+.RE
+.SS "Advanced section"
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutcodon\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+codcopy is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/embossdata.1e
+++ emboss-6.4.0/debian/manpages/embossdata.1e
@@ -0,0 +1,86 @@
+'\" t
+.\"     Title: EMBOSSDATA
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "EMBOSSDATA" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+embossdata \- Find and retrieve EMBOSS data files
+.SH "SYNOPSIS"
+.HP \w'\fBembossdata\fR\ 'u
+\fBembossdata\fR [\fB\-showall\ \fR\fB\fItoggle\fR\fR] \fB\-fetch\ \fR\fB\fIboolean\fR\fR \fB\-filename\ \fR\fB\fIstring\fR\fR \fB\-reject\ \fR\fB\fIselection\fR\fR [\fB\-outfile\ \fR\fB\fIoutfile\fR\fR]
+.HP \w'\fBembossdata\fR\ 'u
+\fBembossdata\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBembossdata\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-showall\fR \fItoggle\fR
+.RS 4
+.RE
+.PP
+\fB\-fetch\fR \fIboolean\fR
+.RS 4
+.RE
+.PP
+\fB\-filename\fR \fIstring\fR
+.RS 4
+This specifies the name of the file that should be fetched into the current directory or searched for in all of the directories that EMBOSS programs search when looking for a data file\&. The name of the file is not altered when it is fetched\&.
+.RE
+.SS "Advanced section"
+.PP
+\fB\-reject\fR \fIselection\fR
+.RS 4
+This specifies the names of the sub\-directories of the EMBOSS data directory that should be ignored when displaying data directories\&. Default value: 3, 5, 6
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+This specifies the name of the file that the results of a search for a file in the various data directories is written to\&. By default these results are written to the screen (stdout)\&. Default value: stdout
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+embossdata is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/pepwindow.1e
+++ emboss-6.4.0/debian/manpages/pepwindow.1e
@@ -0,0 +1,86 @@
+'\" t
+.\"     Title: PEPWINDOW
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "PEPWINDOW" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+pepwindow \- Draw a hydropathy plot for a protein sequence
+.SH "SYNOPSIS"
+.HP \w'\fBpepwindow\fR\ 'u
+\fBpepwindow\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR [\fB\-datafile\ \fR\fB\fIdatafile\fR\fR] [\fB\-length\ \fR\fB\fIinteger\fR\fR] [\fB\-normalize\ \fR\fB\fIboolean\fR\fR] \fB\-graph\ \fR\fB\fIxygraph\fR\fR
+.HP \w'\fBpepwindow\fR\ 'u
+\fBpepwindow\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBpepwindow\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Protein:Properties" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIsequence\fR
+.RS 4
+.RE
+.PP
+\fB\-datafile\fR \fIdatafile\fR
+.RS 4
+Default value: Enakai\&.dat
+.RE
+.SS "Additional section"
+.PP
+\fB\-length\fR \fIinteger\fR
+.RS 4
+Default value: 19
+.RE
+.PP
+\fB\-normalize\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.SS "Output section"
+.PP
+\fB\-graph\fR \fIxygraph\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+pepwindow is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/dbshowdat.1e
+++ emboss-6.4.0/debian/manpages/dbshowdat.1e
@@ -0,0 +1,91 @@
+'\" t
+.\"     Title: DBSHOWDAT
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "DBSHOWDAT" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+dbshowdat \- Show possible database queries that return a given data type
+.SH "SYNOPSIS"
+.HP \w'\fBdbshowdat\fR\ 'u
+\fBdbshowdat\fR \fB\-datatype\ \fR\fB\fIstring\fR\fR \fB\-database\ \fR\fB\fIstring\fR\fR \fB\-identifier\ \fR\fB\fIstring\fR\fR [\fB\-outfile\ \fR\fB\fIoutfile\fR\fR] [\fB\-html\ \fR\fB\fIboolean\fR\fR]
+.HP \w'\fBdbshowdat\fR\ 'u
+\fBdbshowdat\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBdbshowdat\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Information" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-datatype\fR \fIstring\fR
+.RS 4
+This is the name of a retrievable datatype from the catalogue of public databases in the EMBOSS data file DRCAT\&.dat\&. The names are terms from the \*(Aqdata\*(Aq branch of the EDAM ontology, http://edamontology\&.sourceforge\&.net/\&. If you are unsure of the available retrievable datatypes for a given database, use dbtellquery\&. If you have a datatype name but are not sure its valid, use isdbdata\&.
+.RE
+.SS "Required section"
+.SS "Additional section"
+.SS "Advanced section"
+.PP
+\fB\-database\fR \fIstring\fR
+.RS 4
+This is the name of a database from the catalogue of public databases in the EMBOSS data file DRCAT\&.dat\&. If you are unsure of the available databases use dbfind\&. If you have a database name but are not sure its valid, use isdbname\&.
+.RE
+.PP
+\fB\-identifier\fR \fIstring\fR
+.RS 4
+This is a data identifier (e\&.g\&. a sequence accession number) that is used to specify the data (of type \*(Aqdatatype\*(Aq) to retrieve\&. If you\*(Aqre unsure of the data identifier(s) that are used for a given query (database/datatype) use dbtellquery\&. The types of data identifier are listed under the \*(AqData identifier\*(Aq branch of the EDAM ontology (http://edamontology\&.sourceforge\&.net/)\&. For example values, see the catalogue of public databases in the EMBOSS data file DRCAT\&.dat\&. If you have a data identifier but are unsure of its type, use idtell\&.
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+Default value: stdout
+.RE
+.SS "Html section"
+.PP
+\fB\-html\fR \fIboolean\fR
+.RS 4
+If you are sending the output to a file, this will format it for displaying as a table in a WWW document\&. Default value: N
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+dbshowdat is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/cacheebeyesearch.1e
+++ emboss-6.4.0/debian/manpages/cacheebeyesearch.1e
@@ -0,0 +1,72 @@
+'\" t
+.\"     Title: CACHEEBEYESEARCH
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "CACHEEBEYESEARCH" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+cacheebeyesearch \- Generates server cache file for EB\-eye search domains
+.SH "SYNOPSIS"
+.HP \w'\fBcacheebeyesearch\fR\ 'u
+\fBcacheebeyesearch\fR [\fB\-outfile\ \fR\fB\fIoutfile\fR\fR] \fB\-cachefile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBcacheebeyesearch\fR\ 'u
+\fBcacheebeyesearch\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBcacheebeyesearch\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Data resources" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+Default value: stdout
+.RE
+.PP
+\fB\-cachefile\fR \fIoutfile\fR
+.RS 4
+Default value: server\&.$(servername)
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+cacheebeyesearch is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/btwisted.1e
+++ emboss-6.4.0/debian/manpages/btwisted.1e
@@ -0,0 +1,80 @@
+'\" t
+.\"     Title: BTWISTED
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "BTWISTED" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+btwisted \- Calculate the twisting in a B\-DNA sequence
+.SH "SYNOPSIS"
+.HP \w'\fBbtwisted\fR\ 'u
+\fBbtwisted\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR \fB\-angledata\ \fR\fB\fIdatafile\fR\fR \fB\-energydata\ \fR\fB\fIdatafile\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBbtwisted\fR\ 'u
+\fBbtwisted\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBbtwisted\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Properties,Nucleic:Composition,Nucleic:2D structure" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIsequence\fR
+.RS 4
+.RE
+.PP
+\fB\-angledata\fR \fIdatafile\fR
+.RS 4
+Default value: Eangles\&.dat
+.RE
+.PP
+\fB\-energydata\fR \fIdatafile\fR
+.RS 4
+Default value: Eenergy\&.dat
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+btwisted is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/plotcon.1e
+++ emboss-6.4.0/debian/manpages/plotcon.1e
@@ -0,0 +1,82 @@
+'\" t
+.\"     Title: PLOTCON
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "PLOTCON" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+plotcon \- Plot conservation of a sequence alignment
+.SH "SYNOPSIS"
+.HP \w'\fBplotcon\fR\ 'u
+\fBplotcon\fR \fB\-sequences\ \fR\fB\fIseqset\fR\fR [\fB\-scorefile\ \fR\fB\fImatrix\fR\fR] \fB\-winsize\ \fR\fB\fIinteger\fR\fR \fB\-graph\ \fR\fB\fIxygraph\fR\fR
+.HP \w'\fBplotcon\fR\ 'u
+\fBplotcon\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBplotcon\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Alignment:Multiple" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequences\fR \fIseqset\fR
+.RS 4
+File containing a sequence alignment
+.RE
+.PP
+\fB\-scorefile\fR \fImatrix\fR
+.RS 4
+This is the scoring matrix file used when comparing sequences\&. By default it is the file \*(AqEBLOSUM62\*(Aq (for proteins) or the file \*(AqEDNAFULL\*(Aq (for nucleic sequences)\&. These files are found in the \*(Aqdata\*(Aq directory of the EMBOSS installation\&.
+.RE
+.SS "Required section"
+.PP
+\fB\-winsize\fR \fIinteger\fR
+.RS 4
+Number of columns to average alignment quality over\&. The larger this value is, the smoother the plot will be\&. Default value: 4
+.RE
+.SS "Output section"
+.PP
+\fB\-graph\fR \fIxygraph\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+plotcon is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/wossoperation.1e
+++ emboss-6.4.0/debian/manpages/wossoperation.1e
@@ -0,0 +1,139 @@
+'\" t
+.\"     Title: WOSSOPERATION
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "WOSSOPERATION" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+wossoperation \- Finds programs by EDAM operation
+.SH "SYNOPSIS"
+.HP \w'\fBwossoperation\fR\ 'u
+\fBwossoperation\fR \fB\-identifier\ \fR\fB\fIstring\fR\fR [\fB\-explode\ \fR\fB\fIboolean\fR\fR] [\fB\-showkeywords\ \fR\fB\fIboolean\fR\fR] \fB\-sensitive\ \fR\fB\fIboolean\fR\fR \fB\-subclasses\ \fR\fB\fIboolean\fR\fR \fB\-obsolete\ \fR\fB\fIboolean\fR\fR \fB\-emboss\ \fR\fB\fIboolean\fR\fR \fB\-embassy\ \fR\fB\fIboolean\fR\fR \fB\-showembassy\ \fR\fB\fIstring\fR\fR \fB\-colon\ \fR\fB\fIboolean\fR\fR \fB\-gui\ \fR\fB\fIboolean\fR\fR [\fB\-outfile\ \fR\fB\fIoutfile\fR\fR] [\fB\-html\ \fR\fB\fItoggle\fR\fR] [\fB\-groups\ \fR\fB\fIboolean\fR\fR] [\fB\-alphabetic\ \fR\fB\fIboolean\fR\fR]
+.HP \w'\fBwossoperation\fR\ 'u
+\fBwossoperation\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBwossoperation\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Ontology:EDAM,Documentation" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-identifier\fR \fIstring\fR
+.RS 4
+.RE
+.SS "Additional section"
+.PP
+\fB\-explode\fR \fIboolean\fR
+.RS 4
+The groups that EMBOSS applications belong to have two forms, exploded and not exploded\&. The exploded group names are more numerous and often vaguely phrased than the non\-exploded ones\&. The exploded names are formed from definitions of the group names that start like NAME1:NAME2 and which are then expanded into many combinations of the names as: \*(AqNAME1\*(Aq, \*(AqNAME2\*(Aq, \*(AqNAME1 NAME2\*(Aq, NAME2 NAME1\*(Aq\&. The non\-expanded names are simply like: \*(AqNAME1 NAME2\*(Aq\&. Default value: N
+.RE
+.PP
+\fB\-showkeywords\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.SS "Advanced section"
+.PP
+\fB\-sensitive\fR \fIboolean\fR
+.RS 4
+By default, the query keywords are matched against the EDAM term names (and synonyms) only\&. This option also matches the keywords against the EDAM term definitions and will therefore (typically) report more matches\&. Default value: N
+.RE
+.PP
+\fB\-subclasses\fR \fIboolean\fR
+.RS 4
+Extend the query matches to include all terms which are specialisations (EDAM sub\-classes) of the matched type\&. Default value: Y
+.RE
+.PP
+\fB\-obsolete\fR \fIboolean\fR
+.RS 4
+The default behaviour is to not use or return obsolete terms\&. This option if set will include all terms\&. Default value: N
+.RE
+.PP
+\fB\-emboss\fR \fIboolean\fR
+.RS 4
+If you use this option then EMBOSS program documentation will be searched\&. If this option is set to be false, then only the EMBASSY programs will be searched (if the \-embassy option is true)\&. EMBASSY programs are not strictly part of EMBOSS, but use the same code libraries and share the same look and feel, but are generally developed by people who wish the programs to be outside of the GNU Public Licence scheme Default value: Y
+.RE
+.PP
+\fB\-embassy\fR \fIboolean\fR
+.RS 4
+If you use this option then EMBASSY program documentation will be searched\&. If this option is set to be false, then only the EMBOSS programs will be searched (if the \-emboss option is true)\&. EMBASSY programs are not strictly part of EMBOSS, but use the same code libraries and share the same look and feel, but are generally developed by people who wish the programs to be outside of the GNU Public Licence scheme Default value: Y
+.RE
+.PP
+\fB\-showembassy\fR \fIstring\fR
+.RS 4
+If you use this option then this EMBASSY package program documentation will be searched\&. EMBASSY programs are not strictly part of EMBOSS, but use the same code libraries and share the same look and feel, but are generally developed by people who wish the programs to be outside of the GNU Public Licence scheme
+.RE
+.PP
+\fB\-colon\fR \fIboolean\fR
+.RS 4
+The groups that EMBOSS applications belong to up to two levels, for example the primary group \*(AqALIGNMENT\*(Aq has several sub\-groups, or second\-level groups, e\&.g\&.: CONSENSUS, DIFFERENCES, DOT PLOTS, GLOBAL, LOCAL, MULTIPLE\&. To aid programs that parse the output of wossname that require the names of these subgroups, a colon \*(Aq:\*(Aq will be placed between the first and second level of the group name if this option is true\&. Note: This does not apply if the group names have been exploded with the \*(Aqexplode\*(Aq option\&. Default value: N
+.RE
+.PP
+\fB\-gui\fR \fIboolean\fR
+.RS 4
+This option is intended to help those who are designing Graphical User Interfaces to the EMBOSS applications\&. Some EMBOSS programs are inappropriate for running in a GUI, these include other menu programs and interactive editors\&. This option allows you to only report those programs that can be run from a GUI Default value: N
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+Default value: stdout
+.RE
+.SS "Html section"
+.PP
+\fB\-html\fR \fItoggle\fR
+.RS 4
+If you are sending the output to a file, this will format it for displaying as a table in a WWW document\&. Default value: N
+.RE
+.PP
+\fB\-groups\fR \fIboolean\fR
+.RS 4
+If you use this option, then only the group names will be output to the file Default value: N
+.RE
+.PP
+\fB\-alphabetic\fR \fIboolean\fR
+.RS 4
+If you use this option, then you will get a single list of the program names and descriptions instead of the programs being listed in their functional groups\&. Default value: N
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+wossoperation is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/pscan.1e
+++ emboss-6.4.0/debian/manpages/pscan.1e
@@ -0,0 +1,81 @@
+'\" t
+.\"     Title: PSCAN
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "PSCAN" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+pscan \- Scans protein sequence(s) with fingerprints from the PRINTS database
+.SH "SYNOPSIS"
+.HP \w'\fBpscan\fR\ 'u
+\fBpscan\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-emin\ \fR\fB\fIinteger\fR\fR \fB\-emax\ \fR\fB\fIinteger\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBpscan\fR\ 'u
+\fBpscan\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBpscan\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Protein:Motifs" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqall\fR
+.RS 4
+.RE
+.SS "Required section"
+.PP
+\fB\-emin\fR \fIinteger\fR
+.RS 4
+Default value: 2
+.RE
+.PP
+\fB\-emax\fR \fIinteger\fR
+.RS 4
+Default value: 20
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+pscan is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/taxgetup.1e
+++ emboss-6.4.0/debian/manpages/taxgetup.1e
@@ -0,0 +1,77 @@
+'\" t
+.\"     Title: TAXGETUP
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "TAXGETUP" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+taxgetup \- Get parents of taxon(s)
+.SH "SYNOPSIS"
+.HP \w'\fBtaxgetup\fR\ 'u
+\fBtaxgetup\fR \fB\-taxons\ \fR\fB\fItaxon\fR\fR \fB\-hidden\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIouttaxon\fR\fR
+.HP \w'\fBtaxgetup\fR\ 'u
+\fBtaxgetup\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBtaxgetup\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Ontology:Taxonomy" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-taxons\fR \fItaxon\fR
+.RS 4
+.RE
+.SS "Additional section"
+.SS "Advanced section"
+.PP
+\fB\-hidden\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIouttaxon\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+taxgetup is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/martquery.1e
+++ emboss-6.4.0/debian/manpages/martquery.1e
@@ -0,0 +1,97 @@
+'\" t
+.\"     Title: MARTQUERY
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "MARTQUERY" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+martquery \- Perform a biomart query
+.SH "SYNOPSIS"
+.HP \w'\fBmartquery\fR\ 'u
+\fBmartquery\fR \fB\-dataset\ \fR\fB\fIstring\fR\fR \fB\-attributes\ \fR\fB\fIstring\fR\fR \fB\-filters\ \fR\fB\fIstring\fR\fR \fB\-host\ \fR\fB\fIstring\fR\fR \fB\-path\ \fR\fB\fIstring\fR\fR \fB\-port\ \fR\fB\fIinteger\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBmartquery\fR\ 'u
+\fBmartquery\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBmartquery\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-dataset\fR \fIstring\fR
+.RS 4
+Default value: drerio_gene_ensembl
+.RE
+.PP
+\fB\-attributes\fR \fIstring\fR
+.RS 4
+Default value: ensembl_gene_id,ensembl_transcript_id
+.RE
+.PP
+\fB\-filters\fR \fIstring\fR
+.RS 4
+Default value: with_transmembrane_domain
+.RE
+.SS "Advanced section"
+.PP
+\fB\-host\fR \fIstring\fR
+.RS 4
+Default value: www\&.biomart\&.org
+.RE
+.PP
+\fB\-path\fR \fIstring\fR
+.RS 4
+Default value: /biomart/martservice
+.RE
+.PP
+\fB\-port\fR \fIinteger\fR
+.RS 4
+Default value: 80
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+martquery is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/xmltotext.1e
+++ emboss-6.4.0/debian/manpages/xmltotext.1e
@@ -0,0 +1,93 @@
+'\" t
+.\"     Title: XMLTOTEXT
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "XMLTOTEXT" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+xmltotext \- Convert an XML document to a plain text format
+.SH "SYNOPSIS"
+.HP \w'\fBxmltotext\fR\ 'u
+\fBxmltotext\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR \fB\-type\ \fR\fB\fIlist\fR\fR \fB\-seq\ \fR\fB\fIlist\fR\fR \fB\-feat\ \fR\fB\fIlist\fR\fR \fB\-align\ \fR\fB\fIlist\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBxmltotext\fR\ 'u
+\fBxmltotext\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBxmltotext\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Misc" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-infile\fR \fIinfile\fR
+.RS 4
+.RE
+.SS "Required section"
+.PP
+\fB\-type\fR \fIlist\fR
+.RS 4
+You must specify the type of file content so that appropriate output format options may be generated\&.
+.RE
+.PP
+\fB\-seq\fR \fIlist\fR
+.RS 4
+This option sets the format of a sequence output file\&. Default value: X
+.RE
+.PP
+\fB\-feat\fR \fIlist\fR
+.RS 4
+This option sets the format of a sequence feature output file\&. Default value: X
+.RE
+.PP
+\fB\-align\fR \fIlist\fR
+.RS 4
+This option sets the format of a sequence alignment output file\&. Default value: X
+.RE
+.SS "Additional section"
+.SS "Advanced section"
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+xmltotext is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/matcher.1e
+++ emboss-6.4.0/debian/manpages/matcher.1e
@@ -0,0 +1,95 @@
+'\" t
+.\"     Title: MATCHER
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "MATCHER" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+matcher \- Waterman\-Eggert local alignment of two sequences
+.SH "SYNOPSIS"
+.HP \w'\fBmatcher\fR\ 'u
+\fBmatcher\fR \fB\-asequence\ \fR\fB\fIsequence\fR\fR \fB\-bsequence\ \fR\fB\fIsequence\fR\fR [\fB\-datafile\ \fR\fB\fImatrix\fR\fR] [\fB\-alternatives\ \fR\fB\fIinteger\fR\fR] [\fB\-gapopen\ \fR\fB\fIinteger\fR\fR] [\fB\-gapextend\ \fR\fB\fIinteger\fR\fR] \fB\-outfile\ \fR\fB\fIalign\fR\fR
+.HP \w'\fBmatcher\fR\ 'u
+\fBmatcher\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBmatcher\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Alignment:Local" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-asequence\fR \fIsequence\fR
+.RS 4
+.RE
+.PP
+\fB\-bsequence\fR \fIsequence\fR
+.RS 4
+.RE
+.PP
+\fB\-datafile\fR \fImatrix\fR
+.RS 4
+This is the scoring matrix file used when comparing sequences\&. By default it is the file \*(AqEBLOSUM62\*(Aq (for proteins) or the file \*(AqEDNAFULL\*(Aq (for nucleic sequences)\&. These files are found in the \*(Aqdata\*(Aq directory of the EMBOSS installation\&.
+.RE
+.SS "Additional section"
+.PP
+\fB\-alternatives\fR \fIinteger\fR
+.RS 4
+This sets the number of alternative matches output\&. By default only the highest scoring alignment is shown\&. A value of 2 gives you other reasonable alignments\&. In some cases, for example multidomain proteins of cDNA and genomic DNA comparisons, there may be other interesting and significant alignments\&. Default value: 1
+.RE
+.PP
+\fB\-gapopen\fR \fIinteger\fR
+.RS 4
+The gap penalty is the score taken away when a gap is created\&. The best value depends on the choice of comparison matrix\&. The default value of 14 assumes you are using the EBLOSUM62 matrix for protein sequences, or a value of 16 and the EDNAFULL matrix for nucleotide sequences\&. Default value: @($(acdprotein)? 14 : 16)
+.RE
+.PP
+\fB\-gapextend\fR \fIinteger\fR
+.RS 4
+The gap length, or gap extension, penalty is added to the standard gap penalty for each base or residue in the gap\&. This is how long gaps are penalized\&. Usually you will expect a few long gaps rather than many short gaps, so the gap extension penalty should be lower than the gap penalty\&. An exception is where one or both sequences are single reads with possible sequencing errors in which case you would expect many single base gaps\&. You can get this result by setting the gap penalty to zero (or very low) and using the gap extension penalty to control gap scoring\&. Default value: @($(acdprotein)? 4 : 4)
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIalign\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+matcher is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/drfinddata.1e
+++ emboss-6.4.0/debian/manpages/drfinddata.1e
@@ -0,0 +1,82 @@
+'\" t
+.\"     Title: DRFINDDATA
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "DRFINDDATA" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+drfinddata \- Find public databases by data type
+.SH "SYNOPSIS"
+.HP \w'\fBdrfinddata\fR\ 'u
+\fBdrfinddata\fR \fB\-query\ \fR\fB\fIstring\fR\fR \fB\-sensitive\ \fR\fB\fIboolean\fR\fR \fB\-subclasses\ \fR\fB\fIboolean\fR\fR \fB\-drfinddata\ \fR\fB\fIoutresource\fR\fR
+.HP \w'\fBdrfinddata\fR\ 'u
+\fBdrfinddata\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBdrfinddata\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Ontology:EDAM,Data retrieval:Resource data" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-query\fR \fIstring\fR
+.RS 4
+.RE
+.SS "Additional section"
+.SS "Advanced section"
+.PP
+\fB\-sensitive\fR \fIboolean\fR
+.RS 4
+By default, the query keywords are matched against the EDAM term names (and synonyms) only\&. This option also matches the keywords against the EDAM term definitions and will therefore (typically) report more matches\&. Default value: N
+.RE
+.PP
+\fB\-subclasses\fR \fIboolean\fR
+.RS 4
+Extend the query matches to include all terms which are specialisations (EDAM sub\-classes) of the matched type\&. Default value: Y
+.RE
+.SS "Output section"
+.PP
+\fB\-drfinddata\fR \fIoutresource\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+drfinddata is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/stssearch.1e
+++ emboss-6.4.0/debian/manpages/stssearch.1e
@@ -0,0 +1,74 @@
+'\" t
+.\"     Title: STSSEARCH
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "STSSEARCH" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+stssearch \- Search a DNA database for matches with a set of STS primers
+.SH "SYNOPSIS"
+.HP \w'\fBstssearch\fR\ 'u
+\fBstssearch\fR \fB\-seqall\ \fR\fB\fIseqall\fR\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBstssearch\fR\ 'u
+\fBstssearch\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBstssearch\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Primers" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-seqall\fR \fIseqall\fR
+.RS 4
+.RE
+.PP
+\fB\-infile\fR \fIinfile\fR
+.RS 4
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+stssearch is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/showfeat.1e
+++ emboss-6.4.0/debian/manpages/showfeat.1e
@@ -0,0 +1,187 @@
+'\" t
+.\"     Title: SHOWFEAT
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "SHOWFEAT" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+showfeat \- Display features of a sequence in pretty format
+.SH "SYNOPSIS"
+.HP \w'\fBshowfeat\fR\ 'u
+\fBshowfeat\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR [\fB\-sourcematch\ \fR\fB\fIstring\fR\fR] [\fB\-typematch\ \fR\fB\fIstring\fR\fR] [\fB\-tagmatch\ \fR\fB\fIstring\fR\fR] [\fB\-valuematch\ \fR\fB\fIstring\fR\fR] [\fB\-sort\ \fR\fB\fIlist\fR\fR] [\fB\-joinfeatures\ \fR\fB\fIboolean\fR\fR] [\fB\-annotation\ \fR\fB\fIrange\fR\fR] \fB\-html\ \fR\fB\fIboolean\fR\fR \fB\-id\ \fR\fB\fIboolean\fR\fR \fB\-description\ \fR\fB\fIboolean\fR\fR \fB\-scale\ \fR\fB\fIboolean\fR\fR \fB\-width\ \fR\fB\fIinteger\fR\fR \fB\-collapse\ \fR\fB\fIboolean\fR\fR \fB\-forward\ \fR\fB\fIboolean\fR\fR \fB\-reverse\ \fR\fB\fIboolean\fR\fR \fB\-unknown\ \fR\fB\fIboolean\fR\fR \fB\-strand\ \fR\fB\fIboolean\fR\fR \fB\-origin\ \fR\fB\fIboolean\fR\fR \fB\-position\ \fR\fB\fIboolean\fR\fR \fB\-type\ \fR\fB\fIboolean\fR\fR \fB\-tags\ \fR\fB\fIboolean\fR\fR \fB\-values\ \fR\fB\fIboolean\fR\fR \fB\-stricttags\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBshowfeat\fR\ 'u
+\fBshowfeat\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBshowfeat\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Display,Feature tables" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIseqall\fR
+.RS 4
+.RE
+.SS "Additional section"
+.PP
+\fB\-sourcematch\fR \fIstring\fR
+.RS 4
+By default any feature source in the feature table is shown\&. You can set this to match any feature source you wish to show\&. The source name is usually either the name of the program that detected the feature or it is the feature table (eg: EMBL) that the feature came from\&. The source may be wildcarded by using \*(Aq*\*(Aq\&. If you wish to show more than one source, separate their names with the character \*(Aq|\*(Aq, eg: gene* | embl Default value: *
+.RE
+.PP
+\fB\-typematch\fR \fIstring\fR
+.RS 4
+By default any feature type in the feature table is shown\&. You can set this to match any feature type you wish to show\&. See http://www\&.ebi\&.ac\&.uk/embl/WebFeat/ for a list of the EMBL feature types and see Appendix A of the Swissprot user manual in http://www\&.expasy\&.org/sprot/userman\&.html for a list of the Swissprot feature types\&. The type may be wildcarded by using \*(Aq*\*(Aq\&. If you wish to show more than one type, separate their names with the character \*(Aq|\*(Aq, eg: *UTR | intron Default value: *
+.RE
+.PP
+\fB\-tagmatch\fR \fIstring\fR
+.RS 4
+Tags are the types of extra values that a feature may have\&. For example in the EMBL feature table, a \*(AqCDS\*(Aq type of feature may have the tags \*(Aq/codon\*(Aq, \*(Aq/codon_start\*(Aq, \*(Aq/db_xref\*(Aq, \*(Aq/EC_number\*(Aq, \*(Aq/evidence\*(Aq, \*(Aq/exception\*(Aq, \*(Aq/function\*(Aq, \*(Aq/gene\*(Aq, \*(Aq/label\*(Aq, \*(Aq/map\*(Aq, \*(Aq/note\*(Aq, \*(Aq/number\*(Aq, \*(Aq/partial\*(Aq, \*(Aq/product\*(Aq, \*(Aq/protein_id\*(Aq, \*(Aq/pseudo\*(Aq, \*(Aq/standard_name\*(Aq, \*(Aq/translation\*(Aq, \*(Aq/transl_except\*(Aq, \*(Aq/transl_table\*(Aq, or \*(Aq/usedin\*(Aq\&. Some of these tags also have values, for example \*(Aq/gene\*(Aq can have the value of the gene name\&. By default any feature tag in the feature table is shown\&. You can set this to match any feature tag you wish to show\&. The tag may be wildcarded by using \*(Aq*\*(Aq\&. If you wish to show more than one tag, separate their names with the character \*(Aq|\*(Aq, eg: gene | label Default value: *
+.RE
+.PP
+\fB\-valuematch\fR \fIstring\fR
+.RS 4
+Tag values are the values associated with a feature tag\&. Tags are the types of extra values that a feature may have\&. For example in the EMBL feature table, a \*(AqCDS\*(Aq type of feature may have the tags \*(Aq/codon\*(Aq, \*(Aq/codon_start\*(Aq, \*(Aq/db_xref\*(Aq, \*(Aq/EC_number\*(Aq, \*(Aq/evidence\*(Aq, \*(Aq/exception\*(Aq, \*(Aq/function\*(Aq, \*(Aq/gene\*(Aq, \*(Aq/label\*(Aq, \*(Aq/map\*(Aq, \*(Aq/note\*(Aq, \*(Aq/number\*(Aq, \*(Aq/partial\*(Aq, \*(Aq/product\*(Aq, \*(Aq/protein_id\*(Aq, \*(Aq/pseudo\*(Aq, \*(Aq/standard_name\*(Aq, \*(Aq/translation\*(Aq, \*(Aq/transl_except\*(Aq, \*(Aq/transl_table\*(Aq, or \*(Aq/usedin\*(Aq\&. Only some of these tags can have values, for example \*(Aq/gene\*(Aq can have the value of the gene name\&. By default any feature tag value in the feature table is shown\&. You can set this to match any feature tag value you wish to show\&. The tag value may be wildcarded by using \*(Aq*\*(Aq\&. If you wish to show more than one tag value, separate their names with the character \*(Aq|\*(Aq, eg: pax* | 10 Default value: *
+.RE
+.PP
+\fB\-sort\fR \fIlist\fR
+.RS 4
+Default value: start
+.RE
+.PP
+\fB\-joinfeatures\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-annotation\fR \fIrange\fR
+.RS 4
+Regions to annotate by marking\&. If this is left blank, then no annotation is added\&. A set of regions is specified by a set of pairs of positions followed by optional text\&. The positions are integers\&. They are followed by any text (but not digits when on the command\-line)\&. Examples of region specifications are: 24\-45 new domain 56\-78 match to Mouse 1\-100 First part 120\-156 oligo A file of ranges to annotate (one range per line) can be specified as \*(Aq@filename\*(Aq\&.
+.RE
+.SS "Advanced section"
+.PP
+\fB\-html\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-id\fR \fIboolean\fR
+.RS 4
+Set this to be false if you do not wish to display the ID name of the sequence\&. Default value: Y
+.RE
+.PP
+\fB\-description\fR \fIboolean\fR
+.RS 4
+Set this to be false if you do not wish to display the description of the sequence\&. Default value: Y
+.RE
+.PP
+\fB\-scale\fR \fIboolean\fR
+.RS 4
+Set this to be false if you do not wish to display the scale line\&. Default value: Y
+.RE
+.PP
+\fB\-width\fR \fIinteger\fR
+.RS 4
+You can expand (or contract) the width of the ASCII\-character graphics display of the positions of the features using this value\&. For example, a width of 80 characters would cover a standard page width and a width a 10 characters would be nearly unreadable\&. If the width is set to less than 4, the graphics lines and the scale line will not be displayed\&. Default value: 60
+.RE
+.PP
+\fB\-collapse\fR \fIboolean\fR
+.RS 4
+If this is set, then features from the same source and of the same type and sense are all printed on the same line\&. For instance if there are several features from the EMBL feature table (ie\&. the same source) which are all of type \*(Aqexon\*(Aq in the same sense, then they will all be displayed on the same line\&. This makes it hard to distinguish overlapping features\&. If this is set to false then each feature is displayed on a separate line making it easier to distinguish where features start and end\&. Default value: N
+.RE
+.PP
+\fB\-forward\fR \fIboolean\fR
+.RS 4
+Set this to be false if you do not wish to display forward sense features\&. Default value: Y
+.RE
+.PP
+\fB\-reverse\fR \fIboolean\fR
+.RS 4
+Set this to be false if you do not wish to display reverse sense features\&. Default value: Y
+.RE
+.PP
+\fB\-unknown\fR \fIboolean\fR
+.RS 4
+Set this to be false if you do not wish to display unknown sense features\&. (ie\&. features with no directionality \- all protein features are of this type and some nucleic features (for example, CG\-rich regions))\&. Default value: Y
+.RE
+.PP
+\fB\-strand\fR \fIboolean\fR
+.RS 4
+Set this if you wish to display the strand of the features\&. Protein features are always directionless (indicated by \*(Aq0\*(Aq), forward is indicated by \*(Aq+\*(Aq and reverse is \*(Aq\-\*(Aq\&. Default value: N
+.RE
+.PP
+\fB\-origin\fR \fIboolean\fR
+.RS 4
+Set this if you wish to display the origin of the features\&. The source name is usually either the name of the program that detected the feature or it is the name of the feature table (eg: EMBL) that the feature came from\&. Default value: N
+.RE
+.PP
+\fB\-position\fR \fIboolean\fR
+.RS 4
+Set this if you wish to display the start and end position of the features\&. If several features are being displayed on the same line, then the start and end positions will be joined by a comma, for example: \*(Aq189\-189,225\-225\*(Aq\&. Default value: N
+.RE
+.PP
+\fB\-type\fR \fIboolean\fR
+.RS 4
+Set this to be false if you do not wish to display the type of the features\&. Default value: Y
+.RE
+.PP
+\fB\-tags\fR \fIboolean\fR
+.RS 4
+Set this to be false if you do not wish to display the tags and values of the features\&. Default value: N
+.RE
+.PP
+\fB\-values\fR \fIboolean\fR
+.RS 4
+Set this to be false if you do not wish to display the tag values of the features\&. If this is set to be false, only the tag names will be displayed\&. If the tags are not displayed, then the values will not be displayed\&. The value of the \*(Aqtranslation\*(Aq tag is never displayed as it is often extremely long\&. Default value: Y
+.RE
+.PP
+\fB\-stricttags\fR \fIboolean\fR
+.RS 4
+By default if any tag/value pair in a feature matches the specified tag and value, then all the tags/value pairs of that feature will be displayed\&. If this is set to be true, then only those tag/value pairs in a feature that match the specified tag and value will be displayed\&. Default value: N
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+showfeat is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/prima.1e
+++ emboss-6.4.0/debian/manpages/prima.1e
@@ -0,0 +1,166 @@
+'\" t
+.\"     Title: PRIMA
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "PRIMA" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+prima \- Selects primers for PCR and DNA amplification\&.
+.SH "SYNOPSIS"
+.HP \w'\fBprima\fR\ 'u
+\fBprima\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR \fB\-targetrange\ \fR\fB\fItoggle\fR\fR \fB\-targetstart\ \fR\fB\fIinteger\fR\fR \fB\-targetend\ \fR\fB\fIinteger\fR\fR \fB\-mintmprimer\ \fR\fB\fIfloat\fR\fR \fB\-maxtmprimer\ \fR\fB\fIfloat\fR\fR \fB\-minplen\ \fR\fB\fIinteger\fR\fR \fB\-maxplen\ \fR\fB\fIinteger\fR\fR \fB\-minpgccont\ \fR\fB\fIfloat\fR\fR \fB\-maxpgccont\ \fR\fB\fIfloat\fR\fR [\fB\-primer\ \fR\fB\fItoggle\fR\fR] \fB\-minprimerlen\ \fR\fB\fIinteger\fR\fR \fB\-maxprimerlen\ \fR\fB\fIinteger\fR\fR \fB\-minpmgccont\ \fR\fB\fIfloat\fR\fR \fB\-maxpmgccont\ \fR\fB\fIfloat\fR\fR \fB\-overlap\ \fR\fB\fIinteger\fR\fR \fB\-saltconc\ \fR\fB\fIfloat\fR\fR \fB\-dnaconc\ \fR\fB\fIfloat\fR\fR \fB\-list\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBprima\fR\ 'u
+\fBprima\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBprima\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Primers" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIsequence\fR
+.RS 4
+.RE
+.SS "Required section"
+.SS "Target options"
+.PP
+\fB\-targetrange\fR \fItoggle\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-targetstart\fR \fIinteger\fR
+.RS 4
+Default value: $(sequence\&.begin)
+.RE
+.PP
+\fB\-targetend\fR \fIinteger\fR
+.RS 4
+Default value: $(sequence\&.length)
+.RE
+.PP
+\fB\-mintmprimer\fR \fIfloat\fR
+.RS 4
+Default value: 53
+.RE
+.PP
+\fB\-maxtmprimer\fR \fIfloat\fR
+.RS 4
+Default value: 58
+.RE
+.SS "Additional section"
+.SS "Product options"
+.PP
+\fB\-minplen\fR \fIinteger\fR
+.RS 4
+Default value: 100
+.RE
+.PP
+\fB\-maxplen\fR \fIinteger\fR
+.RS 4
+Default value: 300
+.RE
+.PP
+\fB\-minpgccont\fR \fIfloat\fR
+.RS 4
+Default value: \&.40
+.RE
+.PP
+\fB\-maxpgccont\fR \fIfloat\fR
+.RS 4
+Default value: \&.55
+.RE
+.SS "Primer options"
+.PP
+\fB\-primer\fR \fItoggle\fR
+.RS 4
+Specify primer properties Default value: Y
+.RE
+.PP
+\fB\-minprimerlen\fR \fIinteger\fR
+.RS 4
+Default value: 18
+.RE
+.PP
+\fB\-maxprimerlen\fR \fIinteger\fR
+.RS 4
+Default value: 22
+.RE
+.PP
+\fB\-minpmgccont\fR \fIfloat\fR
+.RS 4
+Default value: \&.40
+.RE
+.PP
+\fB\-maxpmgccont\fR \fIfloat\fR
+.RS 4
+Default value: \&.55
+.RE
+.SS "Advanced section"
+.PP
+\fB\-overlap\fR \fIinteger\fR
+.RS 4
+Default value: 50
+.RE
+.PP
+\fB\-saltconc\fR \fIfloat\fR
+.RS 4
+Default value: 50
+.RE
+.PP
+\fB\-dnaconc\fR \fIfloat\fR
+.RS 4
+Default value: 50
+.RE
+.PP
+\fB\-list\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+prima is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/docxmlvalid.1e
+++ emboss-6.4.0/debian/manpages/docxmlvalid.1e
@@ -0,0 +1,82 @@
+'\" t
+.\"     Title: DOCXMLVALID
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "DOCXMLVALID" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+docxmlvalid \- Check an XML document is well formed and conforms to a schema
+.SH "SYNOPSIS"
+.HP \w'\fBdocxmlvalid\fR\ 'u
+\fBdocxmlvalid\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR \fB\-schema\ \fR\fB\fIinfile\fR\fR \fB\-validate\ \fR\fB\fIlist\fR\fR \fB\-logfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBdocxmlvalid\fR\ 'u
+\fBdocxmlvalid\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBdocxmlvalid\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Misc" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-infile\fR \fIinfile\fR
+.RS 4
+.RE
+.PP
+\fB\-schema\fR \fIinfile\fR
+.RS 4
+.RE
+.SS "Required section"
+.PP
+\fB\-validate\fR \fIlist\fR
+.RS 4
+This option specifies the type (DTD, XSD or Relax\-NG) of the supplied which will be used to validated the supplied XML file\&. Default value: D
+.RE
+.SS "Additional section"
+.SS "Advanced section"
+.SS "Output section"
+.PP
+\fB\-logfile\fR \fIoutfile\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+docxmlvalid is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/acdrelations.1e
+++ emboss-6.4.0/debian/manpages/acdrelations.1e
@@ -0,0 +1,89 @@
+'\" t
+.\"     Title: ACDRELATIONS
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "ACDRELATIONS" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+acdrelations \- Add relations: attribute to ACD files
+.SH "SYNOPSIS"
+.HP \w'\fBacdrelations\fR\ 'u
+\fBacdrelations\fR \fB\-mode\ \fR\fB\fIlist\fR\fR \fB\-indir\ \fR\fB\fIdirlist\fR\fR \fB\-inedamfile\ \fR\fB\fIdatafile\fR\fR \fB\-intypefile\ \fR\fB\fIinfile\fR\fR \fB\-outdir\ \fR\fB\fIoutdir\fR\fR
+.HP \w'\fBacdrelations\fR\ 'u
+\fBacdrelations\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBacdrelations\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Acd,Data retrieval:Tool data" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-mode\fR \fIlist\fR
+.RS 4
+Default value: 1
+.RE
+.PP
+\fB\-indir\fR \fIdirlist\fR
+.RS 4
+Default value: acdin
+.RE
+.PP
+\fB\-inedamfile\fR \fIdatafile\fR
+.RS 4
+Default value: edamtoacd\&.dat
+.RE
+.PP
+\fB\-intypefile\fR \fIinfile\fR
+.RS 4
+Default value: /homes/jison/emboss/emboss/emboss/acd/knowntypes\&.standard
+.RE
+.SS "Required section"
+.SS "Advanced section"
+.SS "Output section"
+.PP
+\fB\-outdir\fR \fIoutdir\fR
+.RS 4
+Default value: acdout
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+acdrelations is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/cutseq.1e
+++ emboss-6.4.0/debian/manpages/cutseq.1e
@@ -0,0 +1,81 @@
+'\" t
+.\"     Title: CUTSEQ
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\"      Date: 05/11/2012
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.4.0
+.\"  Language: English
+.\"
+.TH "CUTSEQ" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+cutseq \- Removes a section from a sequence
+.SH "SYNOPSIS"
+.HP \w'\fBcutseq\fR\ 'u
+\fBcutseq\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR \fB\-from\ \fR\fB\fIinteger\fR\fR \fB\-to\ \fR\fB\fIinteger\fR\fR \fB\-outseq\ \fR\fB\fIseqout\fR\fR
+.HP \w'\fBcutseq\fR\ 'u
+\fBcutseq\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBcutseq\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-sequence\fR \fIsequence\fR
+.RS 4
+.RE
+.SS "Required section"
+.PP
+\fB\-from\fR \fIinteger\fR
+.RS 4
+This is the start position (inclusive) of the section of the sequence that you wish to remove\&. Default value: $(sequence\&.begin)
+.RE
+.PP
+\fB\-to\fR \fIinteger\fR
+.RS 4
+This is the end position (inclusive) of the section of the sequence that you wish to remove\&. Default value: $(sequence\&.end)
+.RE
+.SS "Output section"
+.PP
+\fB\-outseq\fR \fIseqout\fR
+.RS 4
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+cutseq is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
--- emboss-6.4.0.orig/debian/manpages/showdball.1e
+++ emboss-6.4.0/debian/manpages/showdball.1e
@@ -0,0 +1,139 @@
+'\" t
+.\"     Title: SHOWDBALL
+.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.75.2 <http://docbook.sf.net/>
+.\"      Date: 07/20/2010
+.\"    Manual: EMBOSS Manual for Debian
+.\"    Source: EMBOSS 6.3.1
+.\"  Language: English
+.\"
+.TH "SHOWDBALL" "1e" "07/20/2010" "EMBOSS 6.3.1" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+showdball \- Display information on biological databases
+.SH "SYNOPSIS"
+.HP \w'\fBshowdball\fR\ 'u
+\fBshowdball\fR [\fB\-name\ \fR\fB\fIarraystring\fR\fR] \fB\-dbref\ \fR\fB\fIdatafile\fR\fR \fB\-category\ \fR\fB\fIselection\fR\fR \fB\-edam\ \fR\fB\fIselection\fR\fR \fB\-edam\ \fR\fB\fIselection\fR\fR \fB\-display\ \fR\fB\fIselection\fR\fR [\fB\-html\ \fR\fB\fItoggle\fR\fR] [\fB\-category\ \fR\fB\fIstring\fR\fR] [\fB\-all\ \fR\fB\fItoggle\fR\fR] [\fB\-name\ \fR\fB\fIboolean\fR\fR] [\fB\-server\ \fR\fB\fIboolean\fR\fR] [\fB\-desc\ \fR\fB\fIboolean\fR\fR] \fB\-edam\ \fR\fB\fIboolean\fR\fR \fB\-type\ \fR\fB\fIboolean\fR\fR [\fB\-outfile\ \fR\fB\fIoutfile\fR\fR]
+.HP \w'\fBshowdball\fR\ 'u
+\fBshowdball\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBshowdball\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Display,Information" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-name\fR \fIarraystring\fR
+.RS 4
+Standard names of databases are given in the EMBOSS datafile \*(Aqdbref\&.dat\*(Aq\&.
+.RE
+.PP
+\fB\-dbref\fR \fIdatafile\fR
+.RS 4
+File of database information including identifier, description, type, URL etc\&. Default value: dbref\&.dat
+.RE
+.SS "Required section"
+.PP
+\fB\-category\fR \fIselection\fR
+.RS 4
+This specifies the SwissProt categories of database to display in the output file Default value: 1
+.RE
+.PP
+\fB\-edam\fR \fIselection\fR
+.RS 4
+This specifies the SwissProt categories of database to display in the output file Default value: 1
+.RE
+.PP
+\fB\-edam\fR \fIselection\fR
+.RS 4
+This specifies the SwissProt categories of database to display in the output file Default value: 1
+.RE
+.PP
+\fB\-display\fR \fIselection\fR
+.RS 4
+The output can include named database(s) only (\*(Aqdatabase\*(Aq option), databases in one or more categories from SwissProt (\*(Aqcategory\*(Aq) or the EDAM ontology (\*(Aqedam\*(Aq), or all known databases (\*(Aqall\*(Aq)\&. Default value: database
+.RE
+.SS "Additional section"
+.PP
+\fB\-html\fR \fItoggle\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-category\fR \fIstring\fR
+.RS 4
+.RE
+.PP
+\fB\-all\fR \fItoggle\fR
+.RS 4
+This will display all available columns\&. It can be combined with \-noCOLNMAE to display all but the named columns e\&.g\&. \*(Aq\-full \-nodesc\*(Aq\&. Default value: N
+.RE
+.PP
+\fB\-name\fR \fIboolean\fR
+.RS 4
+This displays the column of database names Default value: Y
+.RE
+.PP
+\fB\-server\fR \fIboolean\fR
+.RS 4
+This displays the column of URLs of database servers Default value: Y
+.RE
+.PP
+\fB\-desc\fR \fIboolean\fR
+.RS 4
+This displays the column of database short descriptions Default value: Y
+.RE
+.SS "Advanced section"
+.PP
+\fB\-edam\fR \fIboolean\fR
+.RS 4
+Default value: $(full)
+.RE
+.PP
+\fB\-type\fR \fIboolean\fR
+.RS 4
+Default value: $(full)
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+Default value: stdout
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+showdball is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
