--- kalign-2.04.orig/debian/reference
+++ kalign-2.04/debian/reference
@@ -0,0 +1,25 @@
+@article{TimoLassmann02012009,
+author = {Lassmann, Timo and Frings, Oliver and Sonnhammer, Erik L. L.},
+title = {{Kalign2: high-performance multiple alignment of protein and nucleotide sequences allowing external features}},
+journal = {Nucl. Acids Res.},
+volume = {37},
+number = {3},
+pages = {858-865},
+doi = {10.1093/nar/gkn1006},
+year = {2009},
+URL = {http://nar.oxfordjournals.org/cgi/content/abstract/37/3/858},
+eprint = {http://nar.oxfordjournals.org/cgi/reprint/37/3/858.pdf}
+}
+@Article{16343337,
+AUTHOR = {Lassmann, Timo and Sonnhammer, Erik},
+TITLE = {Kalign - an accurate and fast multiple sequence alignment algorithm},
+JOURNAL = {BMC Bioinformatics},
+VOLUME = {6},
+YEAR = {2005},
+NUMBER = {1},
+PAGES = {298},
+URL = {http://www.biomedcentral.com/1471-2105/6/298},
+DOI = {10.1186/1471-2105-6-298},
+PubMedID = {16343337},
+ISSN = {1471-2105},
+}
--- kalign-2.04.orig/debian/control
+++ kalign-2.04/debian/control
@@ -0,0 +1,26 @@
+Source: kalign
+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>,
+ David Paleino <d.paleino@gmail.com>,
+ Andreas Tille <tille@debian.org>
+Build-Depends: debhelper (>= 7)
+Standards-Version: 3.8.0
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/kalign/trunk/?rev=0&sc=0
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/kalign/trunk/
+Homepage: http://msa.cgb.ki.se
+
+Package: kalign
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Enhances: t-coffee
+Description: Global and progressive multiple sequence alignment
+ Kalign is a command line tool to perform multiple alignment of
+ biological sequences. It employs the Muth-Manber string-matching
+ algorithm, to improve both the accuracy and speed of the alignment.
+ It uses global, progressive alignment approach, enriched by employing
+ an approximate string-matching algorithm to calculate sequence
+ distances and by incorporating local matches into the otherwise global
+ alignment.
--- kalign-2.04.orig/debian/kalign.1.xml
+++ kalign-2.04/debian/kalign.1.xml
@@ -0,0 +1,344 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<?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"
+"/usr/share/xml/docbook/schema/dtd/4.5/docbookx.dtd" [
+  <!ENTITY dhfirstname "<firstname>Charles</firstname>">
+  <!ENTITY dhsurname   "<surname>Plessy</surname>">
+  <!ENTITY dhdate      "February 25, 2009">
+  <!ENTITY dhsection   "<manvolnum>1</manvolnum>">
+  <!ENTITY dhemail     "<email>plessy@debian.org</email>">
+  <!ENTITY dhusername  "Charles Plessy">
+  <!ENTITY dhucpackage "<refentrytitle>KALIGN</refentrytitle>">
+  <!ENTITY dhpackage   "kalign">
+  <!ENTITY dhrelease   "2.04">
+  <!ENTITY dhtitle     "Kalign User Manual">
+  <!ENTITY debian      "<productname>Debian</productname>">
+  <!ENTITY gnu         "<acronym>GNU</acronym>">
+  <!ENTITY gpl         "&gnu; <acronym>GPL</acronym>">
+]>
+
+<!-- Copyright 2006?2009 Charles Plessy. You can use, copy, and redistribute this manpage under the same terms as kalign itself. -->
+
+<refentry>
+  <refentryinfo>
+    <title>&dhtitle;</title>
+    <productname>&dhpackage;</productname>
+    <releaseinfo role="version">&dhrelease;</releaseinfo>
+    <date>&dhdate;</date>
+    <authorgroup>
+      <author>
+        <firstname>Timo</firstname>
+        <surname>Lassmann</surname>
+        <contrib>Upstream author of Kalign.</contrib>
+        <address>
+          <email>timolassmann@gmail.com</email>
+        </address>
+      </author>
+      <author>
+       &dhfirstname;
+       &dhsurname;
+       <contrib>Wrote the manpage.</contrib>
+       <address>&dhemail;</address>
+      </author>
+    </authorgroup>
+    <copyright>
+      <year>2004</year>
+      <year>2005</year>
+      <year>2006</year>
+      <year>2007</year>
+      <year>2008</year>
+      <holder>Timo Lassmann</holder>
+    </copyright>
+    <legalnotice>
+      <para>
+        Kalign is free software. You can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation.
+      </para>
+      <para>
+        This manual page was written by &dhusername; &dhemail; for the &debian; system (but may be used by others). Permission is granted to copy, distribute and/or modify this document under the same terms as kalign itself.
+      </para>
+      <para>
+        On Debian systems, the complete text of the GNU General Public License version 2 can be found in <filename>/usr/share/common-licenses/GPL-2</filename>.
+      </para>
+    </legalnotice>
+  </refentryinfo>
+  <refmeta>
+    &dhucpackage;
+
+    &dhsection;
+  </refmeta>
+  <refnamediv>
+    <refname>&dhpackage;</refname>
+
+    <refpurpose>performs multiple alignment of biological sequences.</refpurpose>
+  </refnamediv>
+  <refsynopsisdiv>
+    <cmdsynopsis>
+      <command>&dhpackage;</command>
+      <arg>
+        <replaceable>infile.fasta</replaceable>
+      </arg>
+      <arg choice="opt">
+        <replaceable>outfile.fasta</replaceable>
+      </arg>
+      <arg choice="opt">Options</arg>
+    </cmdsynopsis>
+    
+     <cmdsynopsis>
+      <command>&dhpackage;</command>
+      <arg> -i
+        <replaceable>infile.fasta</replaceable>
+      </arg>
+      <arg choice="opt"> -o
+        <replaceable>outfile.fasta</replaceable>
+      </arg>
+      <arg choice="opt">Options</arg>
+    </cmdsynopsis>
+    
+     <cmdsynopsis>
+      <command>&dhpackage;</command>
+      <arg> &lt;
+        <replaceable>infile.fasta</replaceable>
+      </arg>
+      <arg choice="opt"> &gt;
+        <replaceable>outfile.fasta</replaceable>
+      </arg>
+      <arg choice="opt">Options</arg>
+    </cmdsynopsis>
+   
+  </refsynopsisdiv>
+  <refsect1>
+    <title>DESCRIPTION</title>
+    <para><command>Kalign</command> is a command line tool to perform multiple alignment of biological sequences. It employs the Muth?Manber string-matching algorithm, to improve both the accuracy and speed of the alignment. It uses global, progressive alignment approach, enriched by employing an approximate string-matching algorithm to calculate sequence distances and by incorporating local matches into the otherwise global alignment.</para>
+  </refsect1>
+  
+  <refsect1>
+    <title>OPTIONS</title>
+    <variablelist>
+      <varlistentry>
+        <term>
+          <option>-s</option>
+          <option>-gpo</option>
+          <option>-gapopen</option>
+          <option>-gap_open</option>
+          <parameter>x</parameter>
+        </term>
+        <listitem>
+          <para>Gap open penalty<!-- (default 6.0)-->.</para>
+        </listitem>
+      </varlistentry>
+      
+      <varlistentry>
+        <term>
+          <option>-e</option>
+          <option>-gpe</option>
+          <option>-gap_ext</option>
+          <option>-gapextension</option>
+          <parameter>x</parameter>
+        </term>
+        <listitem>
+          <para>Gap extension penalty.</para>
+        </listitem>
+      </varlistentry>
+      
+      <varlistentry>
+        <term>
+          <option>-t</option>
+          <option>-tgpe</option>
+          <option>-terminal_gap_extension_penalty</option>
+          <parameter>x</parameter>
+        </term>
+        <listitem><para>Terminal gap penalties.</para></listitem>
+      </varlistentry>
+      
+      <varlistentry>
+        <term>
+          <option>-m</option>
+          <option>-bonus</option>
+          <option>-matrix_bonus</option>
+          <parameter>x</parameter>
+        </term>
+        <listitem>
+          <para>A constant added to the substitution matrix.</para>
+        </listitem>
+      </varlistentry>
+      
+      <varlistentry>
+        <term>
+          <option>-c</option>
+          <option>-sort</option>
+          <parameter>&lt;input, tree, gaps.&gt;</parameter>
+        </term>
+        <listitem>
+          <para>The order in which the sequences appear in the output alignment.</para>
+        </listitem>
+      </varlistentry>
+      
+      <varlistentry>
+        <term>
+          <option>-g</option>
+          <option>-feature</option>
+        </term>
+        <listitem>
+          <para>
+            Selects feature mode and specifies which features are to be used: e.g. all, maxplp, STRUCT, PFAM-A?
+          </para>
+        </listitem>
+      </varlistentry>
+      
+      <varlistentry>
+        <term>
+	  <option>-same_feature_score</option>
+        </term>
+        <listitem>
+          <para>
+            Score for aligning same features.
+          </para>
+        </listitem>
+      </varlistentry>
+      
+      <varlistentry>
+        <term>
+	  <option>-diff_feature_score</option>
+        </term>
+        <listitem>
+          <para>
+            Penalty for aligning different features.
+          </para>
+        </listitem>
+      </varlistentry>
+      
+      <varlistentry>
+        <term>
+          <option>-d</option>
+          <option>-distance</option>
+          <parameter>&lt;wu, pair&gt;</parameter>
+        </term>
+        <listitem><para>Distance method</para></listitem>
+      </varlistentry>
+      
+      <varlistentry>
+        <term>
+          <option>-b</option>
+          <option>-tree</option>
+          <option>-guide-tree</option>
+          <parameter>&lt;nj, upgma&gt;</parameter>
+        </term>
+        <listitem>
+          <para>Guide tree method.</para>
+        </listitem>
+      </varlistentry>
+      
+      <varlistentry>
+        <term>
+          <option>-z</option>
+          <option>-zcutoff</option>
+        </term>
+        <listitem>
+          <para>
+            Parameter used in the wu-manber based distance calculation.
+          </para>
+        </listitem>
+      </varlistentry>
+      
+      <varlistentry>
+        <term>
+          <option>-i</option>
+          <option>-in</option>
+          <option>-input</option>
+        </term>
+        <listitem>
+          <para>Name of the input file.</para>
+        </listitem>
+      </varlistentry>
+      
+      <varlistentry>
+        <term>
+          <option>-o</option>
+          <option>-out</option>
+          <option>-output</option>
+        </term>
+        <listitem>
+          <para>Name of the output file.</para>
+        </listitem>
+      </varlistentry>
+      
+
+<!--      <varlistentry>
+        <term><option>-p</option>
+          <option>-points</option>
+        </term>
+        <listitem>
+          <para>Wu-Manber algorithm used in both distance calculation and dynamic programming.</para>
+        </listitem>
+      </varlistentry>
+      
+     <varlistentry>
+        <term><option>-w</option>
+        </term>
+        <listitem>
+          <para>Wu-Manber algorithm will not be used at all.</para>
+        </listitem>
+      </varlistentry>
+
+      <varlistentry>
+        <term><option>-f</option>
+          <option>-fast</option>
+        </term>
+        <listitem>
+          <para>Fast heuristic alignment ( recommended for &gt;500 sequences)</para>
+        </listitem>
+      </varlistentry>
+-->
+      <varlistentry>
+        <term>
+          <option>-a</option>
+          <option>-gap_inc</option>
+        </term>
+        <listitem>
+          <para>Increases gap penalties depending on the number of existing gaps.</para>
+        </listitem>
+      </varlistentry>
+      
+      <varlistentry>
+        <term>
+          <option>-f</option>
+          <option>-format</option>
+          <parameter>&lt;fasta, msf, aln, clu, macsim&gt;</parameter>
+        </term>
+        <listitem>
+          <para>The output format.</para>
+        </listitem>
+      </varlistentry>
+      
+      <varlistentry>
+        <term>
+          <option>-q</option>
+          <option>-quiet</option>
+        </term>
+        <listitem>
+          <para>Print nothing to STDERR. Read nothing from STDIN.</para>
+        </listitem>
+      </varlistentry>
+    </variablelist>
+    
+<!--     <para>  In default mode Kalign will use the Wu-Manber algorithm for distance calculation only. (recommended for &lt; 500 sequences)</para>-->
+  </refsect1>
+ 
+  <refsect1>
+    <title>REFERENCES</title>
+    <itemizedlist>
+      <listitem>
+        <para>
+          Timo Lassmann and Erik L.L. Sonnhammer (2005) Kalign - an accurate and fast multiple sequence alignment algorithm. BMC Bioinformatics 6:298
+        </para>
+      </listitem>
+      <listitem>
+        <para>
+	  Timo Lassmann, Oliver Frings and Erik L. L. Sonnhammer (2009) Kalign2: high-performance multiple alignment of protein and nucleotide sequences allowing external features. Nucleic Acid Research 3:858?865.
+        </para>
+      </listitem>
+    </itemizedlist>
+  </refsect1>
+</refentry>
+
--- kalign-2.04.orig/debian/changelog
+++ kalign-2.04/debian/changelog
@@ -0,0 +1,52 @@
+kalign (2.04-1) unstable; urgency=low
+
+  * New upstream release.
+  * debian/copyright made machine-readable.
+  * debian/rules: replaced deprecated dh_clean -k by dh_prep.
+  * debian/control:
+    - Updated my email address (debian/control).
+    - Checked compliance with Policy 3.8.0 (no changes needed).
+    - Using debhelper 7 (also in debian/compat).
+    - Upadated description and moved reference to debian/reference.
+  * debian/kalign.1*: updated the manual pages.
+
+ -- Charles Plessy <plessy@debian.org>  Thu, 26 Feb 2009 00:19:44 +0900
+
+kalign (2.03-2) unstable; urgency=low
+
+  [ Charles Plessy ]
+  * debian/control:
+    - Add Subversion repository URL to debian/control.
+    - Moved the Homepage: field out from the package's description.
+    - Enhances: t-coffee.
+
+  [ David Paleino ]
+  * debian/kalign.1 added - manpages are now statically generated
+  * debian/control:
+    - B-D updated (see above)
+    - added myself to Uploaders
+    - moved XS-Vcs-* fields to Vcs-*
+  * debian/rules:
+    - reflecting static build of manpages
+    - minor changes
+  * Updated to Standards-Version 3.7.3 (no changes needed)
+
+  [ Andreas Tille ]
+  * Added myself to Uploaders
+
+ -- Andreas Tille <tille@debian.org>  Tue, 18 Mar 2008 09:54:17 +0100
+
+kalign (2.03-1) unstable; urgency=low
+
+  * New upstream release.
+  * Mended the watch file.
+  * Updated the manpage.
+
+ -- Charles Plessy <charles-debian-nospam@plessy.org>  Wed, 21 Feb 2007 09:07:33 +0900
+
+kalign (1.04-1) unstable; urgency=low
+
+  * Initial release Closes: #365344
+
+ -- Charles Plessy <charles-debian-nospam@plessy.org>  Sat, 29 Apr 2006 23:02:57 +0900
+
--- kalign-2.04.orig/debian/rules
+++ kalign-2.04/debian/rules
@@ -0,0 +1,67 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+# Build rules for the Debian package kalign
+# This file was originally written by Joey Hess and Craig Small.
+# As a special exception, when this file is copied by dh-make into a
+# dh-make output file, you may use that output file without restriction.
+# This special exception was added by Craig Small in version 0.37 of dh-make.
+# Modifications by Charles Plessy during the years 2006 and 2007
+# are hereby released as "public domain".
+
+CFLAGS = -Wall -g
+
+ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS)))
+	CFLAGS += -O0
+else
+	CFLAGS += -O2
+endif
+
+XP=xsltproc \
+	-o debian/ \
+	-''-nonet /usr/share/xml/docbook/stylesheet/nwalsh/manpages/docbook.xsl
+
+kalign.1: debian/kalign.1.xml
+	$(XP) $<
+
+build: build-stamp
+build-stamp:
+	dh_testdir
+	./configure
+	$(MAKE)
+	touch $@
+
+clean:
+	-rm build-stamp
+	dh_testdir
+	dh_testroot
+	rm -f build-stamp configure-stamp
+	[ ! -f Makefile ] || $(MAKE) clean
+	dh_clean
+
+install: build
+	dh_testdir
+	dh_testroot
+	dh_prep
+	dh_installdirs /usr/bin
+	install -o 755 kalign debian/kalign/usr/bin/
+
+binary-indep:
+
+binary-arch: build install
+	dh_testdir
+	dh_testroot
+	dh_installchangelogs 
+	dh_installdocs README
+	dh_installman debian/kalign.1
+	dh_link
+	dh_strip
+	dh_compress
+	dh_fixperms
+	dh_installdeb
+	dh_shlibdeps
+	dh_gencontrol
+	dh_md5sums
+	dh_builddeb
+
+binary: binary-indep binary-arch
+.PHONY: build clean binary-indep binary-arch binary install configure
--- kalign-2.04.orig/debian/copyright
+++ kalign-2.04/debian/copyright
@@ -0,0 +1,47 @@
+Format-Specification: http://wiki.debian.org/Proposals/CopyrightFormat?action=recall&rev=440
+Upstream-Name: Kalign
+Upstream-Maintainer: Timo Lassmann <timolassmann@gmail.com>
+Upstream-Source: http://msa.cgb.ki.se/downloads/kalign/current.tar.gz
+
+Files : *
+Copyright: © 2004–2008 Timo Lassmann <timolassmann@gmail.com>
+License: GPL-2+
+ This package is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 2 of the License, or
+ (at your option) any later version.
+ .
+ This package 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 General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License
+ along with this package; if not, write to the Free Software
+ Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301 USA
+X-Debian-Comment: On Debian systems, the complete text of the GNU General
+ Public License version 2 can be found in `/usr/share/common-licenses/GPL-2'.
+
+Files: COPYING
+Copyright: © 1989, 1991 Free Software Foundation, Inc.
+License: changing it is not allowed.
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+Files: configure
+Copyright: © 2003 Free Software Foundation, Inc.
+License: unlimited permission to copy, distribute and modify it.
+ This configure script is free software; the Free Software Foundation
+ gives unlimited permission to copy, distribute and modify it.
+
+Files: debian/*
+Copyright: © 2006–2009 Charles Plessy <plessy@debian.org>
+           © 2008 David Paleino <d.paleino@gmail.com>
+           © 2008 Andreas Tille <tille@debian.org>
+Licence: As if in public domain.
+  The packaging work is in the public domain unless stated otherwise.
+
+Files: debian/kalign.1*
+Copyright: © 2006–2009 Charles Plessy <plessy@debian.org>
+License: Same as kalign.
+ (See above)
--- kalign-2.04.orig/debian/kalign.1
+++ kalign-2.04/debian/kalign.1
@@ -0,0 +1,142 @@
+.\"     Title: KALIGN
+.\"    Author: Timo Lassmann <timolassmann@gmail.com>
+.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
+.\"      Date: February 25, 2009
+.\"    Manual: Kalign User Manual
+.\"    Source: kalign 2.04
+.\"
+.TH "KALIGN" "1" "February 25, 2009" "kalign 2.04" "Kalign User Manual"
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.SH "NAME"
+kalign \- performs multiple alignment of biological sequences.
+.SH "SYNOPSIS"
+.HP 7
+\fBkalign\fR [\fIinfile\&.fasta\fR] [\fIoutfile\&.fasta\fR] [Options]
+.HP 7
+\fBkalign\fR [\-i\ \fIinfile\&.fasta\fR] [\-o\ \fIoutfile\&.fasta\fR] [Options]
+.HP 7
+\fBkalign\fR [<\ \fIinfile\&.fasta\fR] [>\ \fIoutfile\&.fasta\fR] [Options]
+.SH "DESCRIPTION"
+.PP
+\fBKalign\fR
+is a command line tool to perform multiple alignment of biological sequences\&. It employs the Muth?Manber string\-matching algorithm, to improve both the accuracy and speed of the alignment\&. It uses global, progressive alignment approach, enriched by employing an approximate string\-matching algorithm to calculate sequence distances and by incorporating local matches into the otherwise global alignment\&.
+.SH "OPTIONS"
+.PP
+\fB\-s\fR \fB\-gpo\fR \fB\-gapopen\fR \fB\-gap_open\fR \fIx\fR
+.RS 4
+Gap open penalty
+\&.
+.RE
+.PP
+\fB\-e\fR \fB\-gpe\fR \fB\-gap_ext\fR \fB\-gapextension\fR \fIx\fR
+.RS 4
+Gap extension penalty\&.
+.RE
+.PP
+\fB\-t\fR \fB\-tgpe\fR \fB\-terminal_gap_extension_penalty\fR \fIx\fR
+.RS 4
+Terminal gap penalties\&.
+.RE
+.PP
+\fB\-m\fR \fB\-bonus\fR \fB\-matrix_bonus\fR \fIx\fR
+.RS 4
+A constant added to the substitution matrix\&.
+.RE
+.PP
+\fB\-c\fR \fB\-sort\fR \fI<input, tree, gaps\&.>\fR
+.RS 4
+The order in which the sequences appear in the output alignment\&.
+.RE
+.PP
+\fB\-g\fR \fB\-feature\fR
+.RS 4
+Selects feature mode and specifies which features are to be used: e\&.g\&. all, maxplp, STRUCT, PFAM\-A?
+.RE
+.PP
+\fB\-same_feature_score\fR
+.RS 4
+Score for aligning same features\&.
+.RE
+.PP
+\fB\-diff_feature_score\fR
+.RS 4
+Penalty for aligning different features\&.
+.RE
+.PP
+\fB\-d\fR \fB\-distance\fR \fI<wu, pair>\fR
+.RS 4
+Distance method
+.RE
+.PP
+\fB\-b\fR \fB\-tree\fR \fB\-guide\-tree\fR \fI<nj, upgma>\fR
+.RS 4
+Guide tree method\&.
+.RE
+.PP
+\fB\-z\fR \fB\-zcutoff\fR
+.RS 4
+Parameter used in the wu\-manber based distance calculation\&.
+.RE
+.PP
+\fB\-i\fR \fB\-in\fR \fB\-input\fR
+.RS 4
+Name of the input file\&.
+.RE
+.PP
+\fB\-o\fR \fB\-out\fR \fB\-output\fR
+.RS 4
+Name of the output file\&.
+.RE
+.PP
+\fB\-a\fR \fB\-gap_inc\fR
+.RS 4
+Increases gap penalties depending on the number of existing gaps\&.
+.RE
+.PP
+\fB\-f\fR \fB\-format\fR \fI<fasta, msf, aln, clu, macsim>\fR
+.RS 4
+The output format\&.
+.RE
+.PP
+\fB\-q\fR \fB\-quiet\fR
+.RS 4
+Print nothing to STDERR\&. Read nothing from STDIN\&.
+.RE
+.SH "REFERENCES"
+.sp
+.RS 4
+\h'-04'\(bu\h'+03'Timo Lassmann and Erik L\&.L\&. Sonnhammer (2005) Kalign \- an accurate and fast multiple sequence alignment algorithm\&. BMC Bioinformatics 6:298
+.RE
+.sp
+.RS 4
+\h'-04'\(bu\h'+03'Timo Lassmann, Oliver Frings and Erik L\&. L\&. Sonnhammer (2009) Kalign2: high\-performance multiple alignment of protein and nucleotide sequences allowing external features\&. Nucleic Acid Research 3:858?865\&.
+.RE
+.SH "AUTHORS"
+.PP
+\fBTimo Lassmann\fR <\&timolassmann@gmail\&.com\&>
+.sp -1n
+.IP "" 4
+Upstream author of Kalign\&.
+.PP
+\fBCharles Plessy\fR <\&plessy@debian\&.org\&>
+.sp -1n
+.IP "" 4
+Wrote the manpage\&.
+.SH "COPYRIGHT"
+Copyright \(co 2004, 2005, 2006, 2007, 2008 Timo Lassmann
+.br
+.PP
+Kalign is free software\&. You can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation\&.
+.PP
+This manual page was written by Charles Plessy
+<plessy@debian\&.org>
+for the
+Debian(TM)
+system (but may be used by others)\&. Permission is granted to copy, distribute and/or modify this document under the same terms as kalign itself\&.
+.PP
+On Debian systems, the complete text of the GNU General Public License version 2 can be found in
+\fI/usr/share/common\-licenses/GPL\-2\fR\&.
+.sp
--- kalign-2.04.orig/debian/watch
+++ kalign-2.04/debian/watch
@@ -0,0 +1,3 @@
+# There is no more version number: http://msa.cgb.ki.se/downloads/kalign/current.tar.gz
+#version=3
+#http://msa.cgb.ki.se/downloads/ kalign-?(\d).(\d+).tgz
--- kalign-2.04.orig/debian/compat
+++ kalign-2.04/debian/compat
@@ -0,0 +1 @@
+7