--- wise-2.4.1.orig/debian/compat
+++ wise-2.4.1/debian/compat
@@ -0,0 +1 @@
+7
--- wise-2.4.1.orig/debian/dirs
+++ wise-2.4.1/debian/dirs
@@ -0,0 +1 @@
+usr/bin
--- wise-2.4.1.orig/debian/README.Debian
+++ wise-2.4.1/debian/README.Debian
@@ -0,0 +1,7 @@
+wise for Debian
+--------------------------------------------------------------------------------
+
+You may want to copy /usr/share/doc/wise-doc/examles/* (distributed by wise-doc)
+to your home directory and set WISECONFIGDIR appropriately.
+
+ -- Philipp Benner <pbenner@uni-osnabrueck.de>, Mon, 14 Jan 2008 18:36:28 +0100
--- wise-2.4.1.orig/debian/wise-doc.docs
+++ wise-2.4.1/debian/wise-doc.docs
@@ -0,0 +1,6 @@
+docs/api.pdf
+docs/dynamite.pdf
+docs/wise2.pdf
+docs/api
+docs/dynamite
+docs/wise2
--- wise-2.4.1.orig/debian/wise-doc.doc-base.dynamite
+++ wise-2.4.1/debian/wise-doc.doc-base.dynamite
@@ -0,0 +1,13 @@
+Document: wise-dynamite
+Title: Wise dynamite Manual
+Author: Ewan Birney
+Abstract: This manual describes the dynamite code generating
+ language for dynamic programming.
+Section: Science/Biology
+
+Format: PDF
+Files: /usr/share/doc/wise-doc/dynamite.pdf.gz
+
+Format: HTML
+Index: /usr/share/doc/wise-doc/dynamite/dynamite.html
+Files: /usr/share/doc/wise-doc/dynamite/*
--- wise-2.4.1.orig/debian/manpages
+++ wise-2.4.1/debian/manpages
@@ -0,0 +1,12 @@
+debian/manpages.d/dba.1
+debian/manpages.d/dnal.1
+debian/manpages.d/estwise.1
+debian/manpages.d/estwisedb.1
+debian/manpages.d/genewise.1
+debian/manpages.d/genewisedb.1
+debian/manpages.d/genomewise.1
+debian/manpages.d/promoterwise.1
+debian/manpages.d/psw.1
+debian/manpages.d/pswdb.1
+debian/manpages.d/scanwise.1
+debian/manpages.d/scanwise_server.1
--- wise-2.4.1.orig/debian/rules
+++ wise-2.4.1/debian/rules
@@ -0,0 +1,149 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+CFLAGS = -Wall -g
+
+ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS)))
+	CFLAGS += -O0
+else
+	CFLAGS += -O2
+endif
+
+include /usr/share/quilt/quilt.make
+
+configure: configure-stamp
+configure-stamp:
+	dh_testdir
+
+	touch configure-stamp
+
+build: patch build-stamp
+build-stamp: $(QUILT_STAMPFN) configure-stamp
+	dh_testdir
+
+	$(MAKE) -C src all
+	$(MAKE) -C debian/manpages.d
+
+#	build documentation manually (docs/makefile is not useable)
+	cat src/models/*.tex src/dynlibsrc/*.tex | perl docs/gettex.pl > docs/temp.tex
+	cat docs/wise2api.tex docs/temp.tex docs/apiend.tex > docs/api.tex
+#	<bugfix>
+	sed -i 's/ sw_wrap / sw\\_wrap /' docs/api.tex
+	sed -i 's/label{module_sequence\\_codon}/label{module_sequence_codon}/' docs/api.tex
+	sed -i 's/Wise2::GeneParameter21_wrap/Wise2::GeneParameter21\\_wrap/' docs/api.tex
+#	</bugfix>
+	cd docs && pdflatex api.tex
+	cd docs && pdflatex api.tex
+	cd docs && pdflatex dynamite.tex
+	cd docs && pdflatex dynamite.tex
+#	cd docs && ps2pdf genewise6.eps  # segfaults on s390
+#	cd docs && ps2pdf genewise21.eps
+	cd docs && pdflatex wise2.tex
+	cd docs && pdflatex wise2.tex
+
+	cd docs && hevea api.tex
+	cd docs && hevea api.tex
+	cd docs && hevea dynamite.tex
+	cd docs && hevea dynamite.tex
+	cd docs && hevea wise2.tex
+	cd docs && hevea wise2.tex
+
+	mkdir -p docs/api
+	mkdir -p docs/dynamite
+	mkdir -p docs/wise2
+
+	mv docs/api.html docs/api
+	mv docs/dynamite.html docs/dynamite
+	mv docs/wise2.html docs/wise2
+
+	touch $@
+
+clean: unpatch
+	dh_testdir
+	dh_testroot
+	rm -f build-stamp configure-stamp
+
+	$(MAKE) -C src clean
+	$(MAKE) -C debian/manpages.d clean
+
+#	bugfix
+	$(RM) -r src/oldbin
+	for i in dba psw dnal genomewise pswdb scanwise estwise genewise sywise genewisedb promoterwise pseudowise estwisedb; do $(RM) src/modules/$$i; done
+	$(RM) src/network/scanwise_server
+
+#	clean documentation
+	$(RM) docs/temp.tex
+	$(RM) docs/api.*
+	$(RM) docs/wise2.image.tex
+	$(RM) docs/*.pdf
+	$(RM) docs/*.aux
+	$(RM) docs/*.log
+	$(RM) docs/*.toc
+	$(RM) docs/*.pdf
+	$(RM) docs/*.dvi
+	$(RM) docs/*.ps
+	$(RM) docs/*.4ct
+	$(RM) docs/*.4tc
+	$(RM) docs/*.css
+	$(RM) docs/*.idv
+	$(RM) docs/*.lg
+	$(RM) docs/*.tmp
+	$(RM) docs/*.xref
+	$(RM) docs/*.haux
+	$(RM) docs/*.htoc
+	$(RM) docs/*.html
+
+	$(RM) -r docs/api
+	$(RM) -r docs/dynamite
+	$(RM) -r docs/wise2
+
+	dh_clean
+
+install: build
+	dh_testdir
+	dh_testroot
+	dh_prep 
+	dh_installdirs
+
+#	$(MAKE) install DESTDIR=$(CURDIR)/debian/wise
+	install -m 755 src/bin/* debian/wise/usr/bin
+	install -m 755 src/models/genomewise debian/wise/usr/bin
+
+binary-indep: build install
+	dh_testdir -i
+	dh_testroot -i
+	dh_installchangelogs -i
+	dh_installdocs -i
+	dh_installexamples -i
+	dh_installman -i
+	dh_link -i
+	dh_strip -i
+	dh_compress -i
+	dh_fixperms -i
+	dh_installdeb -i
+	dh_gencontrol -i
+	dh_md5sums -i
+	dh_builddeb -i
+
+binary-arch: build install
+	dh_testdir -a
+	dh_testroot -a
+	dh_installchangelogs -a
+	dh_installdocs -a
+	dh_installexamples -a
+	dh_installman -a
+	dh_link -a
+	dh_strip -a
+	dh_compress -a
+	dh_fixperms -a
+	dh_installdeb -a
+	dh_shlibdeps -a
+	dh_gencontrol -a
+	dh_md5sums -a
+	dh_builddeb -a
+
+binary: binary-indep binary-arch
+.PHONY: build clean binary-indep binary-arch binary install configure
--- wise-2.4.1.orig/debian/README.source
+++ wise-2.4.1/debian/README.source
@@ -0,0 +1,19 @@
+01_welcome-csh.patch:
+ Removes dependencies on csh and tcsh.
+
+02_isnumber.patch:
+ Replaces isnumber() with isdigit().
+
+03_doc-nodycache.patch:
+ Bugfix in documentation.
+
+04_wise2-pdflatex-update.patch:
+ Use pdflatex instead of latex.
+
+05_glib2.patch:
+ Use glib2 instead of glib1.
+
+06_getline.patch:
+ Fixes conflicting definitions of getline.
+
+ -- Philipp Benner <philipp@debian.org>, Sat, 31 Oct 2009 21:12:15 +0000
--- wise-2.4.1.orig/debian/wise-doc.doc-base.wise
+++ wise-2.4.1/debian/wise-doc.doc-base.wise
@@ -0,0 +1,12 @@
+Document: wise
+Title: Debian wise2 Manual
+Author: Ewan Birney, Richard Copley
+Abstract: This manual describes wise program usages.
+Section: Science/Biology
+
+Format: PDF
+Files: /usr/share/doc/wise-doc/wise2.pdf.gz
+
+Format: HTML
+Index: /usr/share/doc/wise-doc/wise2/wise2.html
+Files: /usr/share/doc/wise-doc/wise2/*
--- wise-2.4.1.orig/debian/wise-doc.doc-base.api
+++ wise-2.4.1/debian/wise-doc.doc-base.api
@@ -0,0 +1,12 @@
+Document: wise-api
+Title: Wise API Manual
+Author: Ewan Birney
+Abstract: This manual describes the wise API.
+Section: Science/Biology
+
+Format: PDF
+Files: /usr/share/doc/wise-doc/api.pdf.gz
+
+Format: HTML
+Index: /usr/share/doc/wise-doc/api/api.html
+Files: /usr/share/doc/wise-doc/api/*
--- wise-2.4.1.orig/debian/control
+++ wise-2.4.1/debian/control
@@ -0,0 +1,49 @@
+Source: wise
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+Uploaders: Philipp Benner <philipp@debian.org>, Steffen Moeller <moeller@debian.org>, Charles Plessy <plessy@debian.org>
+DM-Upload-Allowed: yes
+Build-Depends: debhelper (>= 7), quilt, texlive-latex-base,
+ texlive-extra-utils, hevea, docbook-to-man, libglib2.0-dev
+Standards-Version: 3.8.3
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/wise/?rev=0&sc=0
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/wise/trunk/
+Homepage: http://www.ebi.ac.uk/~birney/wise2/
+
+Package: wise
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Suggests: wise-doc (= ${source:Version})
+Description: comparison of biopolymers, commonly DNA and protein sequences
+ Wise2 is a package focused on comparisons of biopolymers, commonly DNA
+ and protein sequences. There are many other packages which do
+ this, probably the best known being BLAST package (from NCBI) and the 
+ Fasta package (from Bill Pearson). There are other packages, such as
+ the HMMER package (Sean Eddy) or SAM package (UC Santa Cruz) focused
+ on hidden Markov models (HMMs) of biopolymers.
+ .
+ Wise2's particular forte is the comparison of DNA sequence at the level
+ of its protein translation. This comparison allows the simultaneous
+ prediction of say gene structure with homology based alignment.
+ .
+ Wise2 also contains other algorithms, such as the venerable Smith-Waterman
+ algorithm, or more modern ones such as Stephen Altschul's generalised
+ gap penalties, or even experimental ones developed in house, such as
+ dba. The development of these algorithms is due to the ease of developing
+ such algorithms in the environment used by Wise2. 
+ .
+ Wise2 has also been written with an eye for reuse and maintainability. 
+ Although it is a pure C package you can access its functionality 
+ directly in Perl. Parts of the package (or the entire package) can
+ be used by other C or C++ programs without namespace clashes as all
+ externally linked variables have the unique identifier Wise2 prepended.
+
+Package: wise-doc
+Architecture: all
+Section: doc
+Depends: ${misc:Depends}
+Recommends: wise (= ${source:Version}), xpdf-reader | pdf-viewer
+Description: documentation for the wise package
+ This package contains the documentation for Wise2, a package focused on
+ comparisons of biopolymers, commonly DNA and protein sequences.
--- wise-2.4.1.orig/debian/copyright
+++ wise-2.4.1/debian/copyright
@@ -0,0 +1,70 @@
+Name: Wise2
+Source: http://www.ebi.ac.uk/~birney/wise2/wise2.4.1.tar.gz
+
+Copyright: © 1996-2001 Genome Research Limited (GRL) and
+ Ewan Birney <birney@sanger.ac.uk> and Sean Eddy
+License:
+ All of the documentation and software included in the dyc directory of the
+ Wise2 package directory is copyrighted by Genome Research Limited
+ (GRL) and other individuals where appropriate. This license is modelled
+ after the 'BSD' style license and is appropriate for use by both
+ academic and commercial sites, without placing any restriction on the
+ distribution of source code from other sources with this software.
+ .
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions are
+ met:
+ .
+  1.Redistributions of source code must retain the above copyright
+    notice, this list of conditions and the following disclaimer.
+ .
+  2.Redistributions in binary form must reproduce the above copyright
+    notice, this list of conditions and the following disclaimer in
+    the documentation and/or other materials provided with the
+    distribution.
+ .
+  3.Neither the name GRL nor the names of its contributors may be used
+    to endorse or promote products derived from this software without
+    specific prior written permission.
+ .
+ It is considered polite to indicate where appropriate that software which
+ is developed using this source code includes a statement that it was developed
+ using the Wise2 soure code. This is not a requirement however.
+ .
+ THIS SOFTWARE IS PROVIDED BY THE GRL AND CONTRIBUTORS ``AS IS'' AND
+ ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+ PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE GRL OR CONTRIBUTORS BE
+ LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
+ BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+ WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
+ OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN
+ IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+Files: src/HMMer2/*
+Copyright: © 1992-1996 Sean R. Eddy
+License: GPL-2
+ This source code is distributed under the terms of the
+ GNU General Public License. See the files COPYING and
+ GNULICENSE for details.
+
+Files:
+ src/dynlibsrc/histogram.dy src/dynlibsrc/histogram.pod
+ src/dynlibsrc/histogram.tex
+Copyright: © 1996-1999 Genome Research Limited (GRL) and Sean Eddy
+License: LGPL-any
+
+Files: debian/*
+Copyright: © 2006-2007 Philipp Benner <philipp@debian.org>
+           © 2009 Steffen Moeller <moeller@debian.org>
+           © 2009 Charles Plessy <plessy@debian.org>
+           © 2009 Barry deFreese <bdefreese@debian.org>
+License: GPL-2+
+This package was debianized by Philipp Benner on Sun, 23 Jul 2006.
+
+On Debian GNU/Linux systems, the complete text of the GNU General Public
+License version 2 can be found in `/usr/share/common-licenses/GPL-2' and the
+complete text of the GNU Lesser General Public License can be found in
+`/usr/share/common-licenses/LGPL-3'.
--- wise-2.4.1.orig/debian/docs
+++ wise-2.4.1/debian/docs
@@ -0,0 +1 @@
+README
--- wise-2.4.1.orig/debian/changelog
+++ wise-2.4.1/debian/changelog
@@ -0,0 +1,140 @@
+wise (2.4.1-8ubuntu1) oneiric; urgency=low
+
+  * Fix FTBFS with ld --as-needed. LP: #832935.
+
+ -- Matthias Klose <doko@ubuntu.com>  Mon, 12 Sep 2011 16:34:50 +0200
+
+wise (2.4.1-8) unstable; urgency=low
+
+  * Fixed conflicting definitions of getline(). (Closes: #552821)
+  * Added README.source.
+  * Standards version 3.8.3.
+  * Fixed spelling error in package description.
+
+ -- Philipp Benner <philipp@debian.org>  Sat, 31 Oct 2009 21:25:52 +0000
+
+wise (2.4.1-7) unstable; urgency=low
+
+  [ Steffen Moeller ]
+  * Now builds with glib-2. (Closes: #523715). Special thank to Barry deFreese.
+  * Updated policy to 3.8.1 (no changes required).
+  * fixed api->API lintian warning.
+
+  [ Charles Plessy ]
+  * debian/control:
+    - Added myself to the Uploaders.
+    - Added ${misc:Depends} to the package dependencies.
+    - Using Debhelper 7 (also debian/compat).
+    - Eliminated redundancy between the long descriptions of wise and wise-doc.
+  * Replaced ‘dh_clean -k’ by ‘dh_prep’ in debian/rules.
+
+ -- Charles Plessy <plessy@debian.org>  Mon, 15 Jun 2009 20:49:27 +0900
+
+wise (2.4.1-6) unstable; urgency=low
+
+  * Updated policy to 3.8.0 (no changes required).
+  * wise now suggests wise-doc (downgraded from 'recommends').
+  [ Steffen Moeller ]
+  * Using quilt instead of dpatch.
+  [ Philipp Benner ]
+
+ -- Philipp Benner <pbenner@uni-osnabrueck.de>  Sun, 25 Jan 2009 22:57:27 +0000
+
+wise (2.4.1-5) unstable; urgency=low
+
+  * Removed a bashism in debian/rules (Closes: #478639).
+
+ -- Charles Plessy <plessy@debian.org>  Sun, 04 May 2008 15:19:01 +0900
+
+wise (2.4.1-4) unstable; urgency=low
+
+  * Changed the doc-base section according to the new policy
+    [Charles Plessy].
+    
+ -- Philipp Benner <pbenner@uni-osnabrueck.de>  Mon, 31 Mar 2008 10:07:35 +0200
+
+wise (2.4.1-3) unstable; urgency=low
+
+  * New maintainer e-mail address.
+  * debian/control: Added DM-Upload-Allowed: yes.
+
+ -- Philipp Benner <pbenner@uni-osnabrueck.de>  Mon, 14 Jan 2008 18:33:27 +0100
+
+wise (2.4.1-2) unstable; urgency=low
+
+  * Using official Vcs-Browser and Vcs-Svn fields (debian/control).
+  * Moved the Homepage: field out from the package's description
+  + (Charles Plessy).
+  * Converted copyright file to machine interpretable format.
+  * Changed maintainer to Debian-Med Packaging Team.
+
+ -- Philipp Benner <mail@philipp-benner.de>  Sun, 02 Dec 2007 16:15:50 +0100
+
+wise (2.4.1-1) unstable; urgency=low
+
+  * New upstream release.
+
+ -- Philipp Benner <mail@philipp-benner.de>  Sat, 15 Sep 2007 17:18:49 +0200
+
+wise (2.4.0-3) unstable; urgency=low
+
+  * Removed debtags from debian/control.
+  * Updated package description (Closes: #435904).
+  * Excluded genewise21.eps and genewise6.eps from documentation
+  + (workaround for a bug in gs-esp).
+
+ -- Philipp Benner <mail@philipp-benner.de>  Sun, 05 Aug 2007 20:21:35 +0200
+
+wise (2.4.0-2) unstable; urgency=low
+
+  * Converted wise2.tex to a pdflatex compatible latex file
+  + (workaround for a bug in dvips)
+
+ -- Philipp Benner <mail@philipp-benner.de>  Fri, 27 Jul 2007 18:46:33 +0200
+
+wise (2.4.0-1) unstable; urgency=low
+
+  * New upstream release (Closes: #431392)
+  * New dpatch (02_isnumber): src/models/phasemodel.c: replaces isnumber() by isdigit()
+  * New dpatch (03_doc-nodycache): docs/wise2.tex: minor bugfix
+
+ -- Philipp Benner <mail@philipp-benner.de>  Tue, 24 Jul 2007 11:58:36 +0200
+
+wise (2.2.0-5) unstable; urgency=low
+
+  * Removed obsolete dependencies (Closes: #422123)
+
+ -- Philipp Benner <mail@philipp-benner.de>  Sun,  6 May 2007 22:42:27 +0200
+
+wise (2.2.0-4) unstable; urgency=low
+
+  * Adapted debian-med tags
+  * Uscan support
+  * Migrating to texlive
+  * use /bin/sh instead of /bin/csh in src/welcome.csh
+
+ -- Philipp Benner <mail@philipp-benner.de>  Tue, 27 Mar 2007 19:29:08 +0200
+
+wise (2.2.0-3) unstable; urgency=low
+
+  * package tags
+  * fixed typos in package description
+
+ -- Philipp Benner <mail@philipp-benner.de>  Thu, 21 Sep 2006 14:22:39 +0200
+
+wise (2.2.0-2) unstable; urgency=low
+
+  * removed \ref tags from package description
+  * moved examples to package wise-doc
+  * fixed typo in README.Debian
+  * minor changes in debian/control
+  * fixed typo in package description (Closes: #380451)
+  * new html documentation
+
+ -- Philipp Benner <mail@philipp-benner.de>  Sun, 30 Jul 2006 14:08:20 +0200
+
+wise (2.2.0-1) unstable; urgency=low
+
+  * Initial release (Closes: #379604)
+
+ -- Philipp Benner <mail@philipp-benner.de>  Sun, 23 Jul 2006 17:29:49 +0200
--- wise-2.4.1.orig/debian/wise-doc.examples
+++ wise-2.4.1/debian/wise-doc.examples
@@ -0,0 +1 @@
+wisecfg/*
--- wise-2.4.1.orig/debian/watch
+++ wise-2.4.1/debian/watch
@@ -0,0 +1,4 @@
+version=3
+
+http://www.ebi.ac.uk/~birney/wise2/ (?:./)?wise(.*)\.tar\.gz \
+  debian uupdate
--- wise-2.4.1.orig/debian/manpages.d/dba.sgml
+++ wise-2.4.1/debian/manpages.d/dba.sgml
@@ -0,0 +1,155 @@
+<!doctype refentry PUBLIC "-//OASIS//DTD DocBook V4.1//EN" [
+
+<!-- Process this file with docbook-to-man to generate an nroff manual
+     page: `docbook-to-man manpage.sgml > manpage.1'.  You may view
+     the manual page with: `docbook-to-man manpage.sgml | nroff -man |
+     less'.  A typical entry in a Makefile or Makefile.am is:
+
+manpage.1: manpage.sgml
+	docbook-to-man $< > $@
+
+    
+	The docbook-to-man binary is found in the docbook-to-man package.
+	Please remember that if you create the nroff version in one of the
+	debian/rules file targets (such as build), you will need to include
+	docbook-to-man in your Build-Depends control field.
+
+  -->
+
+
+  <!-- Fill in your name for FIRSTNAME and SURNAME. -->
+  <!ENTITY dhfirstname "<firstname>Philipp</firstname>">
+  <!ENTITY dhsurname   "<surname>Benner</surname>">
+  <!-- Please adjust the date whenever revising the manpage. -->
+  <!ENTITY dhdate      "<date>July 2006</date>">
+  <!-- SECTION should be 1-8, maybe w/ subsection other parameters are
+       allowed: see man(7), man(1). -->
+  <!ENTITY dhsection   "<manvolnum>1</manvolnum>">
+  <!ENTITY dhemail     "<email>mail@philipp-benner.de</email>">
+  <!ENTITY dhusername  "Philipp Benner">
+  <!ENTITY dhucpackage "<refentrytitle>DBA</refentrytitle>">
+  <!ENTITY dhpackage   "dba">
+
+  <!ENTITY debian      "<productname>Debian</productname>">
+  <!ENTITY gnu         "<acronym>GNU</acronym>">
+  <!ENTITY gpl         "&gnu; <acronym>GPL</acronym>">
+]>
+
+<refentry>
+  <refentryinfo>
+    <address>
+      &dhemail;
+    </address>
+    <author>
+      &dhfirstname;
+      &dhsurname;
+    </author>
+    <copyright>
+      <year>2006</year>
+      <holder>&dhusername;</holder>
+    </copyright>
+    &dhdate;
+  </refentryinfo>
+  <refmeta>
+    &dhucpackage;
+
+    &dhsection;
+  </refmeta>
+  <refnamediv>
+    <refname>&dhpackage;</refname>
+
+    <refpurpose>characterising shared regulatory regions of genomic DNA</refpurpose>
+  </refnamediv>
+  <refsynopsisdiv>
+    <cmdsynopsis>
+      <command>&dhpackage;</command>
+
+      <group choice=opt>
+        <arg rep=repeat><replaceable>options</replaceable></arg>
+      </group>
+
+      <group choice=req>
+<!-- 	<arg rep=repeat><replaceable>seq1</replaceable></arg> -->
+<!-- 	<arg rep=repeat><replaceable>seq2</replaceable></arg> -->
+	<arg><replaceable> seq1 seq2</replaceable></arg>
+      </group>
+
+    </cmdsynopsis>
+  </refsynopsisdiv>
+  <refsect1>
+    <title>DESCRIPTION</title>
+
+    <para>dba - standing for Dna Block Aligner, was developped by Niclas Jareborg,
+    Richard Durbin and Ewan Birney for characterising shared regulatory regions
+    of genomic DNA, either in upstream regions or introns of genes</para>
+
+    <para>The idea was that in these regions there would a series of shared motifs,
+    perhaps with one or two insertions or deletions but between motifs there
+    would be any length of sequence.</para>
+    
+    <para>The subsquent model was a 3 state model which was log-odd'd ratio to a null
+    model of their being no examples of a motif in the two sequences.</para>
+
+  </refsect1>
+  <refsect1>
+    <title>OPTIONS</title>
+
+    <variablelist>
+      <varlistentry>
+        <term><option>-h</option>
+          <option>-help</option>
+        </term>
+        <listitem>
+          <para>Show summary of options.</para>
+        </listitem>
+      </varlistentry>
+      <varlistentry>
+        <term><option>-v</option>
+          <option>-version</option>
+        </term>
+        <listitem>
+          <para>Show version of program.</para>
+        </listitem>
+      </varlistentry>
+    </variablelist>
+  </refsect1>
+  <refsect1>
+    <title>SEE ALSO</title>
+
+    <para>dnal (1), estwise (1), estwisedb (1), genewise (1), genewisedb (1), genomewise (1), promoterwise (1), psw (1), pswdb (1), scanwise (1), scanwise_server (1).</para>
+  </refsect1>
+  <refsect1>
+    <title>AUTHOR</title>
+
+    <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 terms of the &gnu; General Public License, Version 2 any 
+      later version published by the Free Software Foundation.
+    </para>
+    <para>
+      On Debian systems, the complete text of the GNU General Public
+      License can be found in /usr/share/common-licenses/GPL.
+    </para>
+
+  </refsect1>
+</refentry>
+
+<!-- Keep this comment at the end of the file
+Local variables:
+mode: sgml
+sgml-omittag:t
+sgml-shorttag:t
+sgml-minimize-attributes:nil
+sgml-always-quote-attributes:t
+sgml-indent-step:2
+sgml-indent-data:t
+sgml-parent-document:nil
+sgml-default-dtd-file:nil
+sgml-exposed-tags:nil
+sgml-local-catalogs:nil
+sgml-local-ecat-files:nil
+End:
+-->
+
+
--- wise-2.4.1.orig/debian/manpages.d/genomewise.sgml
+++ wise-2.4.1/debian/manpages.d/genomewise.sgml
@@ -0,0 +1,144 @@
+<!doctype refentry PUBLIC "-//OASIS//DTD DocBook V4.1//EN" [
+
+<!-- Process this file with docbook-to-man to generate an nroff manual
+     page: `docbook-to-man manpage.sgml > manpage.1'.  You may view
+     the manual page with: `docbook-to-man manpage.sgml | nroff -man |
+     less'.  A typical entry in a Makefile or Makefile.am is:
+
+manpage.1: manpage.sgml
+	docbook-to-man $< > $@
+
+    
+	The docbook-to-man binary is found in the docbook-to-man package.
+	Please remember that if you create the nroff version in one of the
+	debian/rules file targets (such as build), you will need to include
+	docbook-to-man in your Build-Depends control field.
+
+  -->
+
+
+  <!-- Fill in your name for FIRSTNAME and SURNAME. -->
+  <!ENTITY dhfirstname "<firstname>Philipp</firstname>">
+  <!ENTITY dhsurname   "<surname>Benner</surname>">
+  <!-- Please adjust the date whenever revising the manpage. -->
+  <!ENTITY dhdate      "<date>July 2006</date>">
+  <!-- SECTION should be 1-8, maybe w/ subsection other parameters are
+       allowed: see man(7), man(1). -->
+  <!ENTITY dhsection   "<manvolnum>1</manvolnum>">
+  <!ENTITY dhemail     "<email>mail@philipp-benner.de</email>">
+  <!ENTITY dhusername  "Philipp Benner">
+  <!ENTITY dhucpackage "<refentrytitle>GENOMEWISE</refentrytitle>">
+  <!ENTITY dhpackage   "genomewise">
+
+  <!ENTITY debian      "<productname>Debian</productname>">
+  <!ENTITY gnu         "<acronym>GNU</acronym>">
+  <!ENTITY gpl         "&gnu; <acronym>GPL</acronym>">
+]>
+
+<refentry>
+  <refentryinfo>
+    <address>
+      &dhemail;
+    </address>
+    <author>
+      &dhfirstname;
+      &dhsurname;
+    </author>
+    <copyright>
+      <year>2006</year>
+      <holder>&dhusername;</holder>
+    </copyright>
+    &dhdate;
+  </refentryinfo>
+  <refmeta>
+    &dhucpackage;
+
+    &dhsection;
+  </refmeta>
+  <refnamediv>
+    <refname>&dhpackage;</refname>
+
+    <refpurpose>A tool for combining disparate evidence strands</refpurpose>
+  </refnamediv>
+  <refsynopsisdiv>
+    <cmdsynopsis>
+      <command>&dhpackage;</command>
+
+      <group choice=opt>
+        <arg rep=repeat><replaceable>options</replaceable></arg>
+      </group>
+
+      <group choice=req>
+<!-- 	<arg rep=repeat><replaceable>seq1</replaceable></arg> -->
+<!-- 	<arg rep=repeat><replaceable>seq2</replaceable></arg> -->
+	<arg><replaceable> genomic-fasta-file evidence-file</replaceable></arg>
+      </group>
+
+    </cmdsynopsis>
+  </refsynopsisdiv>
+  <refsect1>
+    <title>DESCRIPTION</title>
+
+    <para>not available</para>
+
+  </refsect1>
+  <refsect1>
+    <title>OPTIONS</title>
+
+    <variablelist>
+      <varlistentry>
+        <term><option>-help</option>
+        </term>
+        <listitem>
+          <para>Show summary of options.</para>
+        </listitem>
+      </varlistentry>
+      <varlistentry>
+        <term><option>-version</option>
+        </term>
+        <listitem>
+          <para>Show version of program.</para>
+        </listitem>
+      </varlistentry>
+    </variablelist>
+  </refsect1>
+  <refsect1>
+    <title>SEE ALSO</title>
+
+    <para>dba (1), dnal (1), estwise (1), estwisedb (1), genewise (1), genewisedb (1), promoterwise (1), psw (1), pswdb (1), scanwise (1), scanwise_server (1).</para>
+  </refsect1>
+  <refsect1>
+    <title>AUTHOR</title>
+
+    <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 terms of the &gnu; General Public License, Version 2 any 
+      later version published by the Free Software Foundation.
+    </para>
+    <para>
+      On Debian systems, the complete text of the GNU General Public
+      License can be found in /usr/share/common-licenses/GPL.
+    </para>
+
+  </refsect1>
+</refentry>
+
+<!-- Keep this comment at the end of the file
+Local variables:
+mode: sgml
+sgml-omittag:t
+sgml-shorttag:t
+sgml-minimize-attributes:nil
+sgml-always-quote-attributes:t
+sgml-indent-step:2
+sgml-indent-data:t
+sgml-parent-document:nil
+sgml-default-dtd-file:nil
+sgml-exposed-tags:nil
+sgml-local-catalogs:nil
+sgml-local-ecat-files:nil
+End:
+-->
+
+
--- wise-2.4.1.orig/debian/manpages.d/pswdb.sgml
+++ wise-2.4.1/debian/manpages.d/pswdb.sgml
@@ -0,0 +1,144 @@
+<!doctype refentry PUBLIC "-//OASIS//DTD DocBook V4.1//EN" [
+
+<!-- Process this file with docbook-to-man to generate an nroff manual
+     page: `docbook-to-man manpage.sgml > manpage.1'.  You may view
+     the manual page with: `docbook-to-man manpage.sgml | nroff -man |
+     less'.  A typical entry in a Makefile or Makefile.am is:
+
+manpage.1: manpage.sgml
+	docbook-to-man $< > $@
+
+    
+	The docbook-to-man binary is found in the docbook-to-man package.
+	Please remember that if you create the nroff version in one of the
+	debian/rules file targets (such as build), you will need to include
+	docbook-to-man in your Build-Depends control field.
+
+  -->
+
+
+  <!-- Fill in your name for FIRSTNAME and SURNAME. -->
+  <!ENTITY dhfirstname "<firstname>Philipp</firstname>">
+  <!ENTITY dhsurname   "<surname>Benner</surname>">
+  <!-- Please adjust the date whenever revising the manpage. -->
+  <!ENTITY dhdate      "<date>July 2006</date>">
+  <!-- SECTION should be 1-8, maybe w/ subsection other parameters are
+       allowed: see man(7), man(1). -->
+  <!ENTITY dhsection   "<manvolnum>1</manvolnum>">
+  <!ENTITY dhemail     "<email>mail@philipp-benner.de</email>">
+  <!ENTITY dhusername  "Philipp Benner">
+  <!ENTITY dhucpackage "<refentrytitle>PSWDB</refentrytitle>">
+  <!ENTITY dhpackage   "pswdb">
+
+  <!ENTITY debian      "<productname>Debian</productname>">
+  <!ENTITY gnu         "<acronym>GNU</acronym>">
+  <!ENTITY gpl         "&gnu; <acronym>GPL</acronym>">
+]>
+
+<refentry>
+  <refentryinfo>
+    <address>
+      &dhemail;
+    </address>
+    <author>
+      &dhfirstname;
+      &dhsurname;
+    </author>
+    <copyright>
+      <year>2006</year>
+      <holder>&dhusername;</holder>
+    </copyright>
+    &dhdate;
+  </refentryinfo>
+  <refmeta>
+    &dhucpackage;
+
+    &dhsection;
+  </refmeta>
+  <refnamediv>
+    <refname>&dhpackage;</refname>
+
+    <refpurpose>protein smith waterman database</refpurpose>
+  </refnamediv>
+  <refsynopsisdiv>
+    <cmdsynopsis>
+      <command>&dhpackage;</command>
+
+      <group choice=opt>
+        <arg rep=repeat><replaceable>options</replaceable></arg>
+      </group>
+
+      <group choice=req>
+<!-- 	<arg rep=repeat><replaceable>seq1</replaceable></arg> -->
+<!-- 	<arg rep=repeat><replaceable>seq2</replaceable></arg> -->
+	<arg><replaceable> query_db target_db</replaceable></arg>
+      </group>
+
+    </cmdsynopsis>
+  </refsynopsisdiv>
+  <refsect1>
+    <title>DESCRIPTION</title>
+
+    <para>not available</para>
+
+  </refsect1>
+  <refsect1>
+    <title>OPTIONS</title>
+
+    <variablelist>
+      <varlistentry>
+        <term><option>-help</option>
+        </term>
+        <listitem>
+          <para>Show summary of options.</para>
+        </listitem>
+      </varlistentry>
+      <varlistentry>
+        <term><option>-version</option>
+        </term>
+        <listitem>
+          <para>Show version of program.</para>
+        </listitem>
+      </varlistentry>
+    </variablelist>
+  </refsect1>
+  <refsect1>
+    <title>SEE ALSO</title>
+
+    <para>dba (1), dnal (1), estwise (1), estwisedb (1), genewise (1), genewisedb (1), genomewise (1), promoterwise (1), psw (1), scanwise (1), scanwise_server (1).</para>
+  </refsect1>
+  <refsect1>
+    <title>AUTHOR</title>
+
+    <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 terms of the &gnu; General Public License, Version 2 any 
+      later version published by the Free Software Foundation.
+    </para>
+    <para>
+      On Debian systems, the complete text of the GNU General Public
+      License can be found in /usr/share/common-licenses/GPL.
+    </para>
+
+  </refsect1>
+</refentry>
+
+<!-- Keep this comment at the end of the file
+Local variables:
+mode: sgml
+sgml-omittag:t
+sgml-shorttag:t
+sgml-minimize-attributes:nil
+sgml-always-quote-attributes:t
+sgml-indent-step:2
+sgml-indent-data:t
+sgml-parent-document:nil
+sgml-default-dtd-file:nil
+sgml-exposed-tags:nil
+sgml-local-catalogs:nil
+sgml-local-ecat-files:nil
+End:
+-->
+
+
--- wise-2.4.1.orig/debian/manpages.d/psw.sgml
+++ wise-2.4.1/debian/manpages.d/psw.sgml
@@ -0,0 +1,149 @@
+<!doctype refentry PUBLIC "-//OASIS//DTD DocBook V4.1//EN" [
+
+<!-- Process this file with docbook-to-man to generate an nroff manual
+     page: `docbook-to-man manpage.sgml > manpage.1'.  You may view
+     the manual page with: `docbook-to-man manpage.sgml | nroff -man |
+     less'.  A typical entry in a Makefile or Makefile.am is:
+
+manpage.1: manpage.sgml
+	docbook-to-man $< > $@
+
+    
+	The docbook-to-man binary is found in the docbook-to-man package.
+	Please remember that if you create the nroff version in one of the
+	debian/rules file targets (such as build), you will need to include
+	docbook-to-man in your Build-Depends control field.
+
+  -->
+
+
+  <!-- Fill in your name for FIRSTNAME and SURNAME. -->
+  <!ENTITY dhfirstname "<firstname>Philipp</firstname>">
+  <!ENTITY dhsurname   "<surname>Benner</surname>">
+  <!-- Please adjust the date whenever revising the manpage. -->
+  <!ENTITY dhdate      "<date>July 2006</date>">
+  <!-- SECTION should be 1-8, maybe w/ subsection other parameters are
+       allowed: see man(7), man(1). -->
+  <!ENTITY dhsection   "<manvolnum>1</manvolnum>">
+  <!ENTITY dhemail     "<email>mail@philipp-benner.de</email>">
+  <!ENTITY dhusername  "Philipp Benner">
+  <!ENTITY dhucpackage "<refentrytitle>PSW</refentrytitle>">
+  <!ENTITY dhpackage   "psw">
+
+  <!ENTITY debian      "<productname>Debian</productname>">
+  <!ENTITY gnu         "<acronym>GNU</acronym>">
+  <!ENTITY gpl         "&gnu; <acronym>GPL</acronym>">
+]>
+
+<refentry>
+  <refentryinfo>
+    <address>
+      &dhemail;
+    </address>
+    <author>
+      &dhfirstname;
+      &dhsurname;
+    </author>
+    <copyright>
+      <year>2006</year>
+      <holder>&dhusername;</holder>
+    </copyright>
+    &dhdate;
+  </refentryinfo>
+  <refmeta>
+    &dhucpackage;
+
+    &dhsection;
+  </refmeta>
+  <refnamediv>
+    <refname>&dhpackage;</refname>
+
+    <refpurpose>Protein Smith-Waterman and other comparisons</refpurpose>
+  </refnamediv>
+  <refsynopsisdiv>
+    <cmdsynopsis>
+      <command>&dhpackage;</command>
+
+      <group choice=opt>
+        <arg rep=repeat><replaceable>options</replaceable></arg>
+      </group>
+
+      <group choice=req>
+<!-- 	<arg rep=repeat><replaceable>seq1</replaceable></arg> -->
+<!-- 	<arg rep=repeat><replaceable>seq2</replaceable></arg> -->
+	<arg><replaceable> seq1 seq2</replaceable></arg>
+      </group>
+
+    </cmdsynopsis>
+  </refsynopsisdiv>
+  <refsect1>
+    <title>DESCRIPTION</title>
+
+    <para>
+      psw is a short and sweet program for calculating smith waterman alginments
+      quickly. It was mainly written as C driver to test the underlying code which
+      is more useful in things like the Perl port.
+    </para>
+
+  </refsect1>
+
+  <refsect1>
+    <title>OPTIONS</title>
+
+    <variablelist>
+      <varlistentry>
+        <term><option>-help</option>
+        </term>
+        <listitem>
+          <para>Show summary of options.</para>
+        </listitem>
+      </varlistentry>
+      <varlistentry>
+        <term><option>-version</option>
+        </term>
+        <listitem>
+          <para>Show version of program.</para>
+        </listitem>
+      </varlistentry>
+    </variablelist>
+  </refsect1>
+  <refsect1>
+    <title>SEE ALSO</title>
+
+    <para>dba (1), dnal (1), estwise (1), estwisedb (1), genewise (1), genewisedb (1), genomewise (1), promoterwise (1), pswdb (1), scanwise (1), scanwise_server (1).</para>
+  </refsect1>
+  <refsect1>
+    <title>AUTHOR</title>
+
+    <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 terms of the &gnu; General Public License, Version 2 any 
+      later version published by the Free Software Foundation.
+    </para>
+    <para>
+      On Debian systems, the complete text of the GNU General Public
+      License can be found in /usr/share/common-licenses/GPL.
+    </para>
+
+  </refsect1>
+</refentry>
+
+<!-- Keep this comment at the end of the file
+Local variables:
+mode: sgml
+sgml-omittag:t
+sgml-shorttag:t
+sgml-minimize-attributes:nil
+sgml-always-quote-attributes:t
+sgml-indent-step:2
+sgml-indent-data:t
+sgml-parent-document:nil
+sgml-default-dtd-file:nil
+sgml-exposed-tags:nil
+sgml-local-catalogs:nil
+sgml-local-ecat-files:nil
+End:
+-->
+
+
--- wise-2.4.1.orig/debian/manpages.d/genewise.sgml
+++ wise-2.4.1/debian/manpages.d/genewise.sgml
@@ -0,0 +1,144 @@
+<!doctype refentry PUBLIC "-//OASIS//DTD DocBook V4.1//EN" [
+
+<!-- Process this file with docbook-to-man to generate an nroff manual
+     page: `docbook-to-man manpage.sgml > manpage.1'.  You may view
+     the manual page with: `docbook-to-man manpage.sgml | nroff -man |
+     less'.  A typical entry in a Makefile or Makefile.am is:
+
+manpage.1: manpage.sgml
+	docbook-to-man $< > $@
+
+    
+	The docbook-to-man binary is found in the docbook-to-man package.
+	Please remember that if you create the nroff version in one of the
+	debian/rules file targets (such as build), you will need to include
+	docbook-to-man in your Build-Depends control field.
+
+  -->
+
+
+  <!-- Fill in your name for FIRSTNAME and SURNAME. -->
+  <!ENTITY dhfirstname "<firstname>Philipp</firstname>">
+  <!ENTITY dhsurname   "<surname>Benner</surname>">
+  <!-- Please adjust the date whenever revising the manpage. -->
+  <!ENTITY dhdate      "<date>July 2006</date>">
+  <!-- SECTION should be 1-8, maybe w/ subsection other parameters are
+       allowed: see man(7), man(1). -->
+  <!ENTITY dhsection   "<manvolnum>1</manvolnum>">
+  <!ENTITY dhemail     "<email>mail@philipp-benner.de</email>">
+  <!ENTITY dhusername  "Philipp Benner">
+  <!ENTITY dhucpackage "<refentrytitle>GENEWISE</refentrytitle>">
+  <!ENTITY dhpackage   "genewise">
+
+  <!ENTITY debian      "<productname>Debian</productname>">
+  <!ENTITY gnu         "<acronym>GNU</acronym>">
+  <!ENTITY gpl         "&gnu; <acronym>GPL</acronym>">
+]>
+
+<refentry>
+  <refentryinfo>
+    <address>
+      &dhemail;
+    </address>
+    <author>
+      &dhfirstname;
+      &dhsurname;
+    </author>
+    <copyright>
+      <year>2006</year>
+      <holder>&dhusername;</holder>
+    </copyright>
+    &dhdate;
+  </refentryinfo>
+  <refmeta>
+    &dhucpackage;
+
+    &dhsection;
+  </refmeta>
+  <refnamediv>
+    <refname>&dhpackage;</refname>
+
+    <refpurpose>comparison of a related protein to genomic DNA</refpurpose>
+  </refnamediv>
+  <refsynopsisdiv>
+    <cmdsynopsis>
+      <command>&dhpackage;</command>
+
+      <group choice=opt>
+        <arg rep=repeat><replaceable>options</replaceable></arg>
+      </group>
+
+      <group choice=req>
+<!-- 	<arg rep=repeat><replaceable>seq1</replaceable></arg> -->
+<!-- 	<arg rep=repeat><replaceable>seq2</replaceable></arg> -->
+	<arg><replaceable> protein-file dna-file</replaceable></arg>
+      </group>
+
+    </cmdsynopsis>
+  </refsynopsisdiv>
+  <refsect1>
+    <title>DESCRIPTION</title>
+
+    <para>not available</para>
+
+  </refsect1>
+  <refsect1>
+    <title>OPTIONS</title>
+
+    <variablelist>
+      <varlistentry>
+        <term><option>-help</option>
+        </term>
+        <listitem>
+          <para>Show summary of options.</para>
+        </listitem>
+      </varlistentry>
+      <varlistentry>
+        <term><option>-version</option>
+        </term>
+        <listitem>
+          <para>Show version of program.</para>
+        </listitem>
+      </varlistentry>
+    </variablelist>
+  </refsect1>
+  <refsect1>
+    <title>SEE ALSO</title>
+
+    <para>dba (1), dnal (1), estwise (1), estwisedb (1), genewisedb (1), genomewise (1), promoterwise (1), psw (1), pswdb (1), scanwise (1), scanwise_server (1).</para>
+  </refsect1>
+  <refsect1>
+    <title>AUTHOR</title>
+
+    <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 terms of the &gnu; General Public License, Version 2 any 
+      later version published by the Free Software Foundation.
+    </para>
+    <para>
+      On Debian systems, the complete text of the GNU General Public
+      License can be found in /usr/share/common-licenses/GPL.
+    </para>
+
+  </refsect1>
+</refentry>
+
+<!-- Keep this comment at the end of the file
+Local variables:
+mode: sgml
+sgml-omittag:t
+sgml-shorttag:t
+sgml-minimize-attributes:nil
+sgml-always-quote-attributes:t
+sgml-indent-step:2
+sgml-indent-data:t
+sgml-parent-document:nil
+sgml-default-dtd-file:nil
+sgml-exposed-tags:nil
+sgml-local-catalogs:nil
+sgml-local-ecat-files:nil
+End:
+-->
+
+
--- wise-2.4.1.orig/debian/manpages.d/estwisedb.sgml
+++ wise-2.4.1/debian/manpages.d/estwisedb.sgml
@@ -0,0 +1,144 @@
+<!doctype refentry PUBLIC "-//OASIS//DTD DocBook V4.1//EN" [
+
+<!-- Process this file with docbook-to-man to generate an nroff manual
+     page: `docbook-to-man manpage.sgml > manpage.1'.  You may view
+     the manual page with: `docbook-to-man manpage.sgml | nroff -man |
+     less'.  A typical entry in a Makefile or Makefile.am is:
+
+manpage.1: manpage.sgml
+	docbook-to-man $< > $@
+
+    
+	The docbook-to-man binary is found in the docbook-to-man package.
+	Please remember that if you create the nroff version in one of the
+	debian/rules file targets (such as build), you will need to include
+	docbook-to-man in your Build-Depends control field.
+
+  -->
+
+
+  <!-- Fill in your name for FIRSTNAME and SURNAME. -->
+  <!ENTITY dhfirstname "<firstname>Philipp</firstname>">
+  <!ENTITY dhsurname   "<surname>Benner</surname>">
+  <!-- Please adjust the date whenever revising the manpage. -->
+  <!ENTITY dhdate      "<date>July 2006</date>">
+  <!-- SECTION should be 1-8, maybe w/ subsection other parameters are
+       allowed: see man(7), man(1). -->
+  <!ENTITY dhsection   "<manvolnum>1</manvolnum>">
+  <!ENTITY dhemail     "<email>mail@philipp-benner.de</email>">
+  <!ENTITY dhusername  "Philipp Benner">
+  <!ENTITY dhucpackage "<refentrytitle>ESTWISEDB</refentrytitle>">
+  <!ENTITY dhpackage   "estwisedb">
+
+  <!ENTITY debian      "<productname>Debian</productname>">
+  <!ENTITY gnu         "<acronym>GNU</acronym>">
+  <!ENTITY gpl         "&gnu; <acronym>GPL</acronym>">
+]>
+
+<refentry>
+  <refentryinfo>
+    <address>
+      &dhemail;
+    </address>
+    <author>
+      &dhfirstname;
+      &dhsurname;
+    </author>
+    <copyright>
+      <year>2006</year>
+      <holder>&dhusername;</holder>
+    </copyright>
+    &dhdate;
+  </refentryinfo>
+  <refmeta>
+    &dhucpackage;
+
+    &dhsection;
+  </refmeta>
+  <refnamediv>
+    <refname>&dhpackage;</refname>
+
+    <refpurpose>a database of proteins vs a database of EST/cDNA sequences</refpurpose>
+  </refnamediv>
+  <refsynopsisdiv>
+    <cmdsynopsis>
+      <command>&dhpackage;</command>
+
+      <group choice=opt>
+        <arg rep=repeat><replaceable>options</replaceable></arg>
+      </group>
+
+      <group choice=req>
+<!-- 	<arg rep=repeat><replaceable>seq1</replaceable></arg> -->
+<!-- 	<arg rep=repeat><replaceable>seq2</replaceable></arg> -->
+	<arg><replaceable> protein-input dna-input</replaceable></arg>
+      </group>
+
+    </cmdsynopsis>
+  </refsynopsisdiv>
+  <refsect1>
+    <title>DESCRIPTION</title>
+
+    <para>not available</para>
+
+  </refsect1>
+  <refsect1>
+    <title>OPTIONS</title>
+
+    <variablelist>
+      <varlistentry>
+        <term><option>-help</option>
+        </term>
+        <listitem>
+          <para>Show summary of options.</para>
+        </listitem>
+      </varlistentry>
+      <varlistentry>
+        <term><option>-version</option>
+        </term>
+        <listitem>
+          <para>Show version of program.</para>
+        </listitem>
+      </varlistentry>
+    </variablelist>
+  </refsect1>
+  <refsect1>
+    <title>SEE ALSO</title>
+
+    <para>dba (1), dnal (1), estwise (1), genewise (1), genewisedb (1), genomewise (1), promoterwise (1), psw (1), pswdb (1), scanwise (1), scanwise_server (1).</para>
+  </refsect1>
+  <refsect1>
+    <title>AUTHOR</title>
+
+    <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 terms of the &gnu; General Public License, Version 2 any 
+      later version published by the Free Software Foundation.
+    </para>
+    <para>
+      On Debian systems, the complete text of the GNU General Public
+      License can be found in /usr/share/common-licenses/GPL.
+    </para>
+
+  </refsect1>
+</refentry>
+
+<!-- Keep this comment at the end of the file
+Local variables:
+mode: sgml
+sgml-omittag:t
+sgml-shorttag:t
+sgml-minimize-attributes:nil
+sgml-always-quote-attributes:t
+sgml-indent-step:2
+sgml-indent-data:t
+sgml-parent-document:nil
+sgml-default-dtd-file:nil
+sgml-exposed-tags:nil
+sgml-local-catalogs:nil
+sgml-local-ecat-files:nil
+End:
+-->
+
+
--- wise-2.4.1.orig/debian/manpages.d/scanwise_server.sgml
+++ wise-2.4.1/debian/manpages.d/scanwise_server.sgml
@@ -0,0 +1,144 @@
+<!doctype refentry PUBLIC "-//OASIS//DTD DocBook V4.1//EN" [
+
+<!-- Process this file with docbook-to-man to generate an nroff manual
+     page: `docbook-to-man manpage.sgml > manpage.1'.  You may view
+     the manual page with: `docbook-to-man manpage.sgml | nroff -man |
+     less'.  A typical entry in a Makefile or Makefile.am is:
+
+manpage.1: manpage.sgml
+	docbook-to-man $< > $@
+
+    
+	The docbook-to-man binary is found in the docbook-to-man package.
+	Please remember that if you create the nroff version in one of the
+	debian/rules file targets (such as build), you will need to include
+	docbook-to-man in your Build-Depends control field.
+
+  -->
+
+
+  <!-- Fill in your name for FIRSTNAME and SURNAME. -->
+  <!ENTITY dhfirstname "<firstname>Philipp</firstname>">
+  <!ENTITY dhsurname   "<surname>Benner</surname>">
+  <!-- Please adjust the date whenever revising the manpage. -->
+  <!ENTITY dhdate      "<date>July 2006</date>">
+  <!-- SECTION should be 1-8, maybe w/ subsection other parameters are
+       allowed: see man(7), man(1). -->
+  <!ENTITY dhsection   "<manvolnum>1</manvolnum>">
+  <!ENTITY dhemail     "<email>mail@philipp-benner.de</email>">
+  <!ENTITY dhusername  "Philipp Benner">
+  <!ENTITY dhucpackage "<refentrytitle>SCANWISE_SERVER</refentrytitle>">
+  <!ENTITY dhpackage   "scanwise_server">
+
+  <!ENTITY debian      "<productname>Debian</productname>">
+  <!ENTITY gnu         "<acronym>GNU</acronym>">
+  <!ENTITY gpl         "&gnu; <acronym>GPL</acronym>">
+]>
+
+<refentry>
+  <refentryinfo>
+    <address>
+      &dhemail;
+    </address>
+    <author>
+      &dhfirstname;
+      &dhsurname;
+    </author>
+    <copyright>
+      <year>2006</year>
+      <holder>&dhusername;</holder>
+    </copyright>
+    &dhdate;
+  </refentryinfo>
+  <refmeta>
+    &dhucpackage;
+
+    &dhsection;
+  </refmeta>
+  <refnamediv>
+    <refname>&dhpackage;</refname>
+
+    <refpurpose>Server for scanwise</refpurpose>
+  </refnamediv>
+  <refsynopsisdiv>
+    <cmdsynopsis>
+      <command>&dhpackage;</command>
+
+      <group choice=opt>
+        <arg rep=repeat><replaceable>options</replaceable></arg>
+      </group>
+
+      <group choice=req>
+<!-- 	<arg rep=repeat><replaceable>seq1</replaceable></arg> -->
+<!-- 	<arg rep=repeat><replaceable>seq2</replaceable></arg> -->
+	<arg><replaceable> sequence_file_fasta</replaceable></arg>
+      </group>
+
+    </cmdsynopsis>
+  </refsynopsisdiv>
+  <refsect1>
+    <title>DESCRIPTION</title>
+
+    <para>not available</para>
+
+  </refsect1>
+  <refsect1>
+    <title>OPTIONS</title>
+
+    <variablelist>
+      <varlistentry>
+        <term><option>-help</option>
+        </term>
+        <listitem>
+          <para>Show summary of options.</para>
+        </listitem>
+      </varlistentry>
+      <varlistentry>
+        <term><option>-version</option>
+        </term>
+        <listitem>
+          <para>Show version of program.</para>
+        </listitem>
+      </varlistentry>
+    </variablelist>
+  </refsect1>
+  <refsect1>
+    <title>SEE ALSO</title>
+
+    <para>dba (1), dnal (1), estwise (1), estwisedb (1), genewisedb (1), genomewise (1), promoterwise (1), psw (1), pswdb (1), scanwise (1), scanwise_server (1).</para>
+  </refsect1>
+  <refsect1>
+    <title>AUTHOR</title>
+
+    <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 terms of the &gnu; General Public License, Version 2 any 
+      later version published by the Free Software Foundation.
+    </para>
+    <para>
+      On Debian systems, the complete text of the GNU General Public
+      License can be found in /usr/share/common-licenses/GPL.
+    </para>
+
+  </refsect1>
+</refentry>
+
+<!-- Keep this comment at the end of the file
+Local variables:
+mode: sgml
+sgml-omittag:t
+sgml-shorttag:t
+sgml-minimize-attributes:nil
+sgml-always-quote-attributes:t
+sgml-indent-step:2
+sgml-indent-data:t
+sgml-parent-document:nil
+sgml-default-dtd-file:nil
+sgml-exposed-tags:nil
+sgml-local-catalogs:nil
+sgml-local-ecat-files:nil
+End:
+-->
+
+
--- wise-2.4.1.orig/debian/manpages.d/genewisedb.sgml
+++ wise-2.4.1/debian/manpages.d/genewisedb.sgml
@@ -0,0 +1,144 @@
+<!doctype refentry PUBLIC "-//OASIS//DTD DocBook V4.1//EN" [
+
+<!-- Process this file with docbook-to-man to generate an nroff manual
+     page: `docbook-to-man manpage.sgml > manpage.1'.  You may view
+     the manual page with: `docbook-to-man manpage.sgml | nroff -man |
+     less'.  A typical entry in a Makefile or Makefile.am is:
+
+manpage.1: manpage.sgml
+	docbook-to-man $< > $@
+
+    
+	The docbook-to-man binary is found in the docbook-to-man package.
+	Please remember that if you create the nroff version in one of the
+	debian/rules file targets (such as build), you will need to include
+	docbook-to-man in your Build-Depends control field.
+
+  -->
+
+
+  <!-- Fill in your name for FIRSTNAME and SURNAME. -->
+  <!ENTITY dhfirstname "<firstname>Philipp</firstname>">
+  <!ENTITY dhsurname   "<surname>Benner</surname>">
+  <!-- Please adjust the date whenever revising the manpage. -->
+  <!ENTITY dhdate      "<date>July 2006</date>">
+  <!-- SECTION should be 1-8, maybe w/ subsection other parameters are
+       allowed: see man(7), man(1). -->
+  <!ENTITY dhsection   "<manvolnum>1</manvolnum>">
+  <!ENTITY dhemail     "<email>mail@philipp-benner.de</email>">
+  <!ENTITY dhusername  "Philipp Benner">
+  <!ENTITY dhucpackage "<refentrytitle>GENEWISEDB</refentrytitle>">
+  <!ENTITY dhpackage   "genewise">
+
+  <!ENTITY debian      "<productname>Debian</productname>">
+  <!ENTITY gnu         "<acronym>GNU</acronym>">
+  <!ENTITY gpl         "&gnu; <acronym>GPL</acronym>">
+]>
+
+<refentry>
+  <refentryinfo>
+    <address>
+      &dhemail;
+    </address>
+    <author>
+      &dhfirstname;
+      &dhsurname;
+    </author>
+    <copyright>
+      <year>2006</year>
+      <holder>&dhusername;</holder>
+    </copyright>
+    &dhdate;
+  </refentryinfo>
+  <refmeta>
+    &dhucpackage;
+
+    &dhsection;
+  </refmeta>
+  <refnamediv>
+    <refname>&dhpackage;</refname>
+
+    <refpurpose>a database of proteins vs a database of genomic dna sequences</refpurpose>
+  </refnamediv>
+  <refsynopsisdiv>
+    <cmdsynopsis>
+      <command>&dhpackage;</command>
+
+      <group choice=opt>
+        <arg rep=repeat><replaceable>options</replaceable></arg>
+      </group>
+
+      <group choice=req>
+<!-- 	<arg rep=repeat><replaceable>seq1</replaceable></arg> -->
+<!-- 	<arg rep=repeat><replaceable>seq2</replaceable></arg> -->
+	<arg><replaceable> protein-input dna-input</replaceable></arg>
+      </group>
+
+    </cmdsynopsis>
+  </refsynopsisdiv>
+  <refsect1>
+    <title>DESCRIPTION</title>
+
+    <para>not available</para>
+
+  </refsect1>
+  <refsect1>
+    <title>OPTIONS</title>
+
+    <variablelist>
+      <varlistentry>
+        <term><option>-help</option>
+        </term>
+        <listitem>
+          <para>Show summary of options.</para>
+        </listitem>
+      </varlistentry>
+      <varlistentry>
+        <term><option>-version</option>
+        </term>
+        <listitem>
+          <para>Show version of program.</para>
+        </listitem>
+      </varlistentry>
+    </variablelist>
+  </refsect1>
+  <refsect1>
+    <title>SEE ALSO</title>
+
+    <para>dba (1), dnal (1), estwise (1), estwisedb (1), genewise (1), genomewise (1), promoterwise (1), psw (1), pswdb (1), scanwise (1), scanwise_server (1).</para>
+  </refsect1>
+  <refsect1>
+    <title>AUTHOR</title>
+
+    <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 terms of the &gnu; General Public License, Version 2 any 
+      later version published by the Free Software Foundation.
+    </para>
+    <para>
+      On Debian systems, the complete text of the GNU General Public
+      License can be found in /usr/share/common-licenses/GPL.
+    </para>
+
+  </refsect1>
+</refentry>
+
+<!-- Keep this comment at the end of the file
+Local variables:
+mode: sgml
+sgml-omittag:t
+sgml-shorttag:t
+sgml-minimize-attributes:nil
+sgml-always-quote-attributes:t
+sgml-indent-step:2
+sgml-indent-data:t
+sgml-parent-document:nil
+sgml-default-dtd-file:nil
+sgml-exposed-tags:nil
+sgml-local-catalogs:nil
+sgml-local-ecat-files:nil
+End:
+-->
+
+
--- wise-2.4.1.orig/debian/manpages.d/promoterwise.sgml
+++ wise-2.4.1/debian/manpages.d/promoterwise.sgml
@@ -0,0 +1,144 @@
+<!doctype refentry PUBLIC "-//OASIS//DTD DocBook V4.1//EN" [
+
+<!-- Process this file with docbook-to-man to generate an nroff manual
+     page: `docbook-to-man manpage.sgml > manpage.1'.  You may view
+     the manual page with: `docbook-to-man manpage.sgml | nroff -man |
+     less'.  A typical entry in a Makefile or Makefile.am is:
+
+manpage.1: manpage.sgml
+	docbook-to-man $< > $@
+
+    
+	The docbook-to-man binary is found in the docbook-to-man package.
+	Please remember that if you create the nroff version in one of the
+	debian/rules file targets (such as build), you will need to include
+	docbook-to-man in your Build-Depends control field.
+
+  -->
+
+
+  <!-- Fill in your name for FIRSTNAME and SURNAME. -->
+  <!ENTITY dhfirstname "<firstname>Philipp</firstname>">
+  <!ENTITY dhsurname   "<surname>Benner</surname>">
+  <!-- Please adjust the date whenever revising the manpage. -->
+  <!ENTITY dhdate      "<date>July 2006</date>">
+  <!-- SECTION should be 1-8, maybe w/ subsection other parameters are
+       allowed: see man(7), man(1). -->
+  <!ENTITY dhsection   "<manvolnum>1</manvolnum>">
+  <!ENTITY dhemail     "<email>mail@philipp-benner.de</email>">
+  <!ENTITY dhusername  "Philipp Benner">
+  <!ENTITY dhucpackage "<refentrytitle>PROMOTERWISE</refentrytitle>">
+  <!ENTITY dhpackage   "promoterwise">
+
+  <!ENTITY debian      "<productname>Debian</productname>">
+  <!ENTITY gnu         "<acronym>GNU</acronym>">
+  <!ENTITY gpl         "&gnu; <acronym>GPL</acronym>">
+]>
+
+<refentry>
+  <refentryinfo>
+    <address>
+      &dhemail;
+    </address>
+    <author>
+      &dhfirstname;
+      &dhsurname;
+    </author>
+    <copyright>
+      <year>2007</year>
+      <holder>&dhusername;</holder>
+    </copyright>
+    &dhdate;
+  </refentryinfo>
+  <refmeta>
+    &dhucpackage;
+
+    &dhsection;
+  </refmeta>
+  <refnamediv>
+    <refname>&dhpackage;</refname>
+
+    <refpurpose>comparison between two promoter sequences</refpurpose>
+  </refnamediv>
+  <refsynopsisdiv>
+    <cmdsynopsis>
+      <command>&dhpackage;</command>
+
+      <group choice=opt>
+        <arg rep=repeat><replaceable>options</replaceable></arg>
+      </group>
+
+      <group choice=req>
+<!-- 	<arg rep=repeat><replaceable>seq1</replaceable></arg> -->
+<!-- 	<arg rep=repeat><replaceable>seq2</replaceable></arg> -->
+	<arg><replaceable> query_sequence target_sequence</replaceable></arg>
+      </group>
+
+    </cmdsynopsis>
+  </refsynopsisdiv>
+  <refsect1>
+    <title>DESCRIPTION</title>
+
+    <para>not available</para>
+
+  </refsect1>
+  <refsect1>
+    <title>OPTIONS</title>
+
+    <variablelist>
+      <varlistentry>
+        <term><option>-help</option>
+        </term>
+        <listitem>
+          <para>Show summary of options.</para>
+        </listitem>
+      </varlistentry>
+      <varlistentry>
+        <term><option>-version</option>
+        </term>
+        <listitem>
+          <para>Show version of program.</para>
+        </listitem>
+      </varlistentry>
+    </variablelist>
+  </refsect1>
+  <refsect1>
+    <title>SEE ALSO</title>
+
+    <para>dba (1), dnal (1), estwise (1), estwisedb (1), genewisedb (1), genomewise (1), psw (1), pswdb (1) scanwise (1) scanwise_server (1).</para>
+  </refsect1>
+  <refsect1>
+    <title>AUTHOR</title>
+
+    <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 terms of the &gnu; General Public License, Version 2 any 
+      later version published by the Free Software Foundation.
+    </para>
+    <para>
+      On Debian systems, the complete text of the GNU General Public
+      License can be found in /usr/share/common-licenses/GPL.
+    </para>
+
+  </refsect1>
+</refentry>
+
+<!-- Keep this comment at the end of the file
+Local variables:
+mode: sgml
+sgml-omittag:t
+sgml-shorttag:t
+sgml-minimize-attributes:nil
+sgml-always-quote-attributes:t
+sgml-indent-step:2
+sgml-indent-data:t
+sgml-parent-document:nil
+sgml-default-dtd-file:nil
+sgml-exposed-tags:nil
+sgml-local-catalogs:nil
+sgml-local-ecat-files:nil
+End:
+-->
+
+
--- wise-2.4.1.orig/debian/manpages.d/scanwise.sgml
+++ wise-2.4.1/debian/manpages.d/scanwise.sgml
@@ -0,0 +1,144 @@
+<!doctype refentry PUBLIC "-//OASIS//DTD DocBook V4.1//EN" [
+
+<!-- Process this file with docbook-to-man to generate an nroff manual
+     page: `docbook-to-man manpage.sgml > manpage.1'.  You may view
+     the manual page with: `docbook-to-man manpage.sgml | nroff -man |
+     less'.  A typical entry in a Makefile or Makefile.am is:
+
+manpage.1: manpage.sgml
+	docbook-to-man $< > $@
+
+    
+	The docbook-to-man binary is found in the docbook-to-man package.
+	Please remember that if you create the nroff version in one of the
+	debian/rules file targets (such as build), you will need to include
+	docbook-to-man in your Build-Depends control field.
+
+  -->
+
+
+  <!-- Fill in your name for FIRSTNAME and SURNAME. -->
+  <!ENTITY dhfirstname "<firstname>Philipp</firstname>">
+  <!ENTITY dhsurname   "<surname>Benner</surname>">
+  <!-- Please adjust the date whenever revising the manpage. -->
+  <!ENTITY dhdate      "<date>July 2006</date>">
+  <!-- SECTION should be 1-8, maybe w/ subsection other parameters are
+       allowed: see man(7), man(1). -->
+  <!ENTITY dhsection   "<manvolnum>1</manvolnum>">
+  <!ENTITY dhemail     "<email>mail@philipp-benner.de</email>">
+  <!ENTITY dhusername  "Philipp Benner">
+  <!ENTITY dhucpackage "<refentrytitle>SCANWISE</refentrytitle>">
+  <!ENTITY dhpackage   "scanwise">
+
+  <!ENTITY debian      "<productname>Debian</productname>">
+  <!ENTITY gnu         "<acronym>GNU</acronym>">
+  <!ENTITY gpl         "&gnu; <acronym>GPL</acronym>">
+]>
+
+<refentry>
+  <refentryinfo>
+    <address>
+      &dhemail;
+    </address>
+    <author>
+      &dhfirstname;
+      &dhsurname;
+    </author>
+    <copyright>
+      <year>2007</year>
+      <holder>&dhusername;</holder>
+    </copyright>
+    &dhdate;
+  </refentryinfo>
+  <refmeta>
+    &dhucpackage;
+
+    &dhsection;
+  </refmeta>
+  <refnamediv>
+    <refname>&dhpackage;</refname>
+
+    <refpurpose>Fast but sensitive search method for biopolymers</refpurpose>
+  </refnamediv>
+  <refsynopsisdiv>
+    <cmdsynopsis>
+      <command>&dhpackage;</command>
+
+      <group choice=opt>
+        <arg rep=repeat><replaceable>options</replaceable></arg>
+      </group>
+
+      <group choice=req>
+<!-- 	<arg rep=repeat><replaceable>seq1</replaceable></arg> -->
+<!-- 	<arg rep=repeat><replaceable>seq2</replaceable></arg> -->
+	<arg><replaceable> query_sequence_file_fasta</replaceable></arg>
+      </group>
+
+    </cmdsynopsis>
+  </refsynopsisdiv>
+  <refsect1>
+    <title>DESCRIPTION</title>
+
+    <para>not available</para>
+
+  </refsect1>
+  <refsect1>
+    <title>OPTIONS</title>
+
+    <variablelist>
+      <varlistentry>
+        <term><option>-help</option>
+        </term>
+        <listitem>
+          <para>Show summary of options.</para>
+        </listitem>
+      </varlistentry>
+      <varlistentry>
+        <term><option>-version</option>
+        </term>
+        <listitem>
+          <para>Show version of program.</para>
+        </listitem>
+      </varlistentry>
+    </variablelist>
+  </refsect1>
+  <refsect1>
+    <title>SEE ALSO</title>
+
+    <para>dba (1), dnal (1), estwise (1), estwisedb (1), genewisedb (1), genomewise (1), promoterwise (1), psw (1), pswdb (1), scanwise_server (1).</para>
+  </refsect1>
+  <refsect1>
+    <title>AUTHOR</title>
+
+    <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 terms of the &gnu; General Public License, Version 2 any 
+      later version published by the Free Software Foundation.
+    </para>
+    <para>
+      On Debian systems, the complete text of the GNU General Public
+      License can be found in /usr/share/common-licenses/GPL.
+    </para>
+
+  </refsect1>
+</refentry>
+
+<!-- Keep this comment at the end of the file
+Local variables:
+mode: sgml
+sgml-omittag:t
+sgml-shorttag:t
+sgml-minimize-attributes:nil
+sgml-always-quote-attributes:t
+sgml-indent-step:2
+sgml-indent-data:t
+sgml-parent-document:nil
+sgml-default-dtd-file:nil
+sgml-exposed-tags:nil
+sgml-local-catalogs:nil
+sgml-local-ecat-files:nil
+End:
+-->
+
+
--- wise-2.4.1.orig/debian/manpages.d/Makefile
+++ wise-2.4.1/debian/manpages.d/Makefile
@@ -0,0 +1,13 @@
+SHELL		= /bin/sh
+
+MANPAGES	= dba.1 dnal.1 estwise.1 estwisedb.1 genewise.1 genewisedb.1 genomewise.1 promoterwise.1 psw.1 pswdb.1 scanwise.1 scanwise_server.1
+
+all: $(MANPAGES)
+
+$(MANPAGES): %.1 : %.sgml
+	docbook-to-man $< > $@
+
+clean:
+	$(RM) $(MANPAGES)
+
+.PHONY: all
--- wise-2.4.1.orig/debian/manpages.d/dnal.sgml
+++ wise-2.4.1/debian/manpages.d/dnal.sgml
@@ -0,0 +1,144 @@
+<!doctype refentry PUBLIC "-//OASIS//DTD DocBook V4.1//EN" [
+
+<!-- Process this file with docbook-to-man to generate an nroff manual
+     page: `docbook-to-man manpage.sgml > manpage.1'.  You may view
+     the manual page with: `docbook-to-man manpage.sgml | nroff -man |
+     less'.  A typical entry in a Makefile or Makefile.am is:
+
+manpage.1: manpage.sgml
+	docbook-to-man $< > $@
+
+    
+	The docbook-to-man binary is found in the docbook-to-man package.
+	Please remember that if you create the nroff version in one of the
+	debian/rules file targets (such as build), you will need to include
+	docbook-to-man in your Build-Depends control field.
+
+  -->
+
+
+  <!-- Fill in your name for FIRSTNAME and SURNAME. -->
+  <!ENTITY dhfirstname "<firstname>Philipp</firstname>">
+  <!ENTITY dhsurname   "<surname>Benner</surname>">
+  <!-- Please adjust the date whenever revising the manpage. -->
+  <!ENTITY dhdate      "<date>July 2006</date>">
+  <!-- SECTION should be 1-8, maybe w/ subsection other parameters are
+       allowed: see man(7), man(1). -->
+  <!ENTITY dhsection   "<manvolnum>1</manvolnum>">
+  <!ENTITY dhemail     "<email>mail@philipp-benner.de</email>">
+  <!ENTITY dhusername  "Philipp Benner">
+  <!ENTITY dhucpackage "<refentrytitle>DNAL</refentrytitle>">
+  <!ENTITY dhpackage   "dnal">
+
+  <!ENTITY debian      "<productname>Debian</productname>">
+  <!ENTITY gnu         "<acronym>GNU</acronym>">
+  <!ENTITY gpl         "&gnu; <acronym>GPL</acronym>">
+]>
+
+<refentry>
+  <refentryinfo>
+    <address>
+      &dhemail;
+    </address>
+    <author>
+      &dhfirstname;
+      &dhsurname;
+    </author>
+    <copyright>
+      <year>2006</year>
+      <holder>&dhusername;</holder>
+    </copyright>
+    &dhdate;
+  </refentryinfo>
+  <refmeta>
+    &dhucpackage;
+
+    &dhsection;
+  </refmeta>
+  <refnamediv>
+    <refname>&dhpackage;</refname>
+
+    <refpurpose>...</refpurpose>
+  </refnamediv>
+  <refsynopsisdiv>
+    <cmdsynopsis>
+      <command>&dhpackage;</command>
+
+      <group choice=opt>
+        <arg rep=repeat><replaceable>options</replaceable></arg>
+      </group>
+
+      <group choice=req>
+<!-- 	<arg rep=repeat><replaceable>seq1</replaceable></arg> -->
+<!-- 	<arg rep=repeat><replaceable>seq2</replaceable></arg> -->
+	<arg><replaceable> dna-file dna-file</replaceable></arg>
+      </group>
+
+    </cmdsynopsis>
+  </refsynopsisdiv>
+  <refsect1>
+    <title>DESCRIPTION</title>
+
+    <para>not available</para>
+
+  </refsect1>
+  <refsect1>
+    <title>OPTIONS</title>
+
+    <variablelist>
+      <varlistentry>
+        <term><option>-help</option>
+        </term>
+        <listitem>
+          <para>Show summary of options.</para>
+        </listitem>
+      </varlistentry>
+      <varlistentry>
+        <term><option>-version</option>
+        </term>
+        <listitem>
+          <para>Show version of program.</para>
+        </listitem>
+      </varlistentry>
+    </variablelist>
+  </refsect1>
+  <refsect1>
+    <title>SEE ALSO</title>
+
+    <para>dba (1), estwise (1), estwisedb (1), genewise (1), genewisedb (1), genomewise (1), promoterwise (1), psw (1), pswdb (1), scanwise (1), scanwise_server (1).</para>
+  </refsect1>
+  <refsect1>
+    <title>AUTHOR</title>
+
+    <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 terms of the &gnu; General Public License, Version 2 any 
+      later version published by the Free Software Foundation.
+    </para>
+    <para>
+      On Debian systems, the complete text of the GNU General Public
+      License can be found in /usr/share/common-licenses/GPL.
+    </para>
+
+  </refsect1>
+</refentry>
+
+<!-- Keep this comment at the end of the file
+Local variables:
+mode: sgml
+sgml-omittag:t
+sgml-shorttag:t
+sgml-minimize-attributes:nil
+sgml-always-quote-attributes:t
+sgml-indent-step:2
+sgml-indent-data:t
+sgml-parent-document:nil
+sgml-default-dtd-file:nil
+sgml-exposed-tags:nil
+sgml-local-catalogs:nil
+sgml-local-ecat-files:nil
+End:
+-->
+
+
--- wise-2.4.1.orig/debian/manpages.d/estwise.sgml
+++ wise-2.4.1/debian/manpages.d/estwise.sgml
@@ -0,0 +1,144 @@
+<!doctype refentry PUBLIC "-//OASIS//DTD DocBook V4.1//EN" [
+
+<!-- Process this file with docbook-to-man to generate an nroff manual
+     page: `docbook-to-man manpage.sgml > manpage.1'.  You may view
+     the manual page with: `docbook-to-man manpage.sgml | nroff -man |
+     less'.  A typical entry in a Makefile or Makefile.am is:
+
+manpage.1: manpage.sgml
+	docbook-to-man $< > $@
+
+    
+	The docbook-to-man binary is found in the docbook-to-man package.
+	Please remember that if you create the nroff version in one of the
+	debian/rules file targets (such as build), you will need to include
+	docbook-to-man in your Build-Depends control field.
+
+  -->
+
+
+  <!-- Fill in your name for FIRSTNAME and SURNAME. -->
+  <!ENTITY dhfirstname "<firstname>Philipp</firstname>">
+  <!ENTITY dhsurname   "<surname>Benner</surname>">
+  <!-- Please adjust the date whenever revising the manpage. -->
+  <!ENTITY dhdate      "<date>July 2006</date>">
+  <!-- SECTION should be 1-8, maybe w/ subsection other parameters are
+       allowed: see man(7), man(1). -->
+  <!ENTITY dhsection   "<manvolnum>1</manvolnum>">
+  <!ENTITY dhemail     "<email>mail@philipp-benner.de</email>">
+  <!ENTITY dhusername  "Philipp Benner">
+  <!ENTITY dhucpackage "<refentrytitle>ESTWISE</refentrytitle>">
+  <!ENTITY dhpackage   "estwise">
+
+  <!ENTITY debian      "<productname>Debian</productname>">
+  <!ENTITY gnu         "<acronym>GNU</acronym>">
+  <!ENTITY gpl         "&gnu; <acronym>GPL</acronym>">
+]>
+
+<refentry>
+  <refentryinfo>
+    <address>
+      &dhemail;
+    </address>
+    <author>
+      &dhfirstname;
+      &dhsurname;
+    </author>
+    <copyright>
+      <year>2006</year>
+      <holder>&dhusername;</holder>
+    </copyright>
+    &dhdate;
+  </refentryinfo>
+  <refmeta>
+    &dhucpackage;
+
+    &dhsection;
+  </refmeta>
+  <refnamediv>
+    <refname>&dhpackage;</refname>
+
+    <refpurpose>comparison of a related protein to cDNA (or ESTs)</refpurpose>
+  </refnamediv>
+  <refsynopsisdiv>
+    <cmdsynopsis>
+      <command>&dhpackage;</command>
+
+      <group choice=opt>
+        <arg rep=repeat><replaceable>options</replaceable></arg>
+      </group>
+
+      <group choice=req>
+<!-- 	<arg rep=repeat><replaceable>seq1</replaceable></arg> -->
+<!-- 	<arg rep=repeat><replaceable>seq2</replaceable></arg> -->
+	<arg><replaceable> protein-file dna-file</replaceable></arg>
+      </group>
+
+    </cmdsynopsis>
+  </refsynopsisdiv>
+  <refsect1>
+    <title>DESCRIPTION</title>
+
+    <para>not available</para>
+
+  </refsect1>
+  <refsect1>
+    <title>OPTIONS</title>
+
+    <variablelist>
+      <varlistentry>
+        <term><option>-help</option>
+        </term>
+        <listitem>
+          <para>Show summary of options.</para>
+        </listitem>
+      </varlistentry>
+      <varlistentry>
+        <term><option>-version</option>
+        </term>
+        <listitem>
+          <para>Show version of program.</para>
+        </listitem>
+      </varlistentry>
+    </variablelist>
+  </refsect1>
+  <refsect1>
+    <title>SEE ALSO</title>
+
+    <para>dba (1), dnal (1), estwisedb (1), genewise (1), genewisedb (1), genomewise (1), promoterwise (1), psw (1), pswdb (1), scanwise (1), scanwise_server (1).</para>
+  </refsect1>
+  <refsect1>
+    <title>AUTHOR</title>
+
+    <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 terms of the &gnu; General Public License, Version 2 any 
+      later version published by the Free Software Foundation.
+    </para>
+    <para>
+      On Debian systems, the complete text of the GNU General Public
+      License can be found in /usr/share/common-licenses/GPL.
+    </para>
+
+  </refsect1>
+</refentry>
+
+<!-- Keep this comment at the end of the file
+Local variables:
+mode: sgml
+sgml-omittag:t
+sgml-shorttag:t
+sgml-minimize-attributes:nil
+sgml-always-quote-attributes:t
+sgml-indent-step:2
+sgml-indent-data:t
+sgml-parent-document:nil
+sgml-default-dtd-file:nil
+sgml-exposed-tags:nil
+sgml-local-catalogs:nil
+sgml-local-ecat-files:nil
+End:
+-->
+
+
--- wise-2.4.1.orig/debian/patches/02_isnumber.patch
+++ wise-2.4.1/debian/patches/02_isnumber.patch
@@ -0,0 +1,18 @@
+#! /bin/sh /usr/share/dpatch/dpatch-run
+## 02_isnumber.dpatch by Philipp Benner <mail@philipp-benner.de>
+##
+## DP: Replace isnumber() (which does not exist on linux) by isdigit().
+
+@DPATCH@
+diff -urNad wise-2.4.0~/src/models/phasemodel.c wise-2.4.0/src/models/phasemodel.c
+--- wise-2.4.0~/src/models/phasemodel.c	2007-07-01 22:44:39.000000000 +0200
++++ wise-2.4.0/src/models/phasemodel.c	2007-07-16 00:24:16.000000000 +0200
+@@ -20,7 +20,7 @@
+     if( line[0] == '#' ) {
+       continue;
+     }
+-    if( !isnumber(line[0]) ) {
++    if( !isdigit(line[0]) ) {
+       warn("Bad looking line in intron file, %s",line);
+       continue;
+     }
--- wise-2.4.1.orig/debian/patches/06_getline.patch
+++ wise-2.4.1/debian/patches/06_getline.patch
@@ -0,0 +1,302 @@
+Index: wise-2.4.1/src/HMMer2/sqio.c
+===================================================================
+--- wise-2.4.1.orig/src/HMMer2/sqio.c	2009-10-31 20:10:25.000000000 +0000
++++ wise-2.4.1/src/HMMer2/sqio.c	2009-10-31 20:11:11.000000000 +0000
+@@ -213,7 +213,7 @@
+     }
+ }
+ 
+-/* Function: getline()
++/* Function: getline_()
+  * Date:     SRE, Tue Mar  3 08:30:01 1998 [St. Louis]
+  *
+  * Purpose:  read a line from a sequence file into V->sbuffer.
+@@ -229,7 +229,7 @@
+  * Returns:  (void)
+  */
+ static void 
+-getline(struct ReadSeqVars *V)
++getline_(struct ReadSeqVars *V)
+ {
+   char *cp;
+   
+@@ -299,7 +299,7 @@
+   V->seqlen = 0;
+   if (addfirst) addseq(V->sbuffer, V);
+   do {
+-    getline(V);
++    getline_(V);
+ 	/* feof() alone is a bug; files not necessarily \n terminated */
+     if (*(V->sbuffer) == '\0' && feof(V->f))
+       done = TRUE;
+@@ -327,7 +327,7 @@
+   char *sptr;
+ 				/* load first line of entry  */
+   while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0)
+-    getline(V);
++    getline_(V);
+   if (feof(V->f)) return;
+ 
+   if ((sptr = strtok(V->sbuffer + 15, "\n\t ")) != NULL)
+@@ -336,7 +336,7 @@
+       SetSeqinfoString(V->sqinfo, sptr, SQINFO_ID);
+     }
+   do {
+-    getline(V);
++    getline_(V);
+     if (!feof(V->f) && strncmp(V->sbuffer, "TITLE", 5) == 0)
+       SetSeqinfoString(V->sqinfo, V->sbuffer+15, SQINFO_DESC);
+     else if (!feof(V->f) && strncmp(V->sbuffer, "ACCESSION", 9) == 0)
+@@ -345,7 +345,7 @@
+ 	  SetSeqinfoString(V->sqinfo, sptr, SQINFO_ACC);
+       }
+   } while (! feof(V->f) && (strncmp(V->sbuffer,"SEQUENCE", 8) != 0));
+-  getline(V);			/* skip next line, coords */
++  getline_(V);			/* skip next line, coords */
+ 
+   readLoop(0, endPIR, V);
+ 
+@@ -359,7 +359,7 @@
+   /* get next line
+    */
+   while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0)
+-    getline(V);
++    getline_(V);
+ }
+ 
+ 
+@@ -377,7 +377,7 @@
+   char *nm;
+ 				/* position past ';' comments */
+   do {
+-    getline(V);
++    getline_(V);
+   } while (! (feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer != ';')) ));
+ 
+   if (!feof(V->f))
+@@ -389,7 +389,7 @@
+     }
+   
+   while (!(feof(V->f) || ((*V->sbuffer != '\0') && (*V->sbuffer == ';'))))
+-    getline(V);
++    getline_(V);
+ }
+ 
+ static int 
+@@ -411,7 +411,7 @@
+ 	  if ((nm = strtok(V->sbuffer+16, ",\n\t ")) != NULL)
+ 	    SetSeqinfoString(V->sqinfo, nm, SQINFO_NAME);
+ 	}
+-      getline(V);
++      getline_(V);
+     }
+ 
+   if (! feof(V->f))
+@@ -420,7 +420,7 @@
+   /* load next line
+    */
+   while ((!feof(V->f)) && (*V->sbuffer != ';')) 
+-    getline(V);
++    getline_(V);
+ }
+ 
+ 
+@@ -438,7 +438,7 @@
+   int   in_definition;
+ 
+   while (strncmp(V->sbuffer, "LOCUS", 5) != 0)
+-    getline(V);
++    getline_(V);
+ 
+   if ((sptr = strtok(V->sbuffer+12, "\n\t ")) != NULL)
+     {
+@@ -449,7 +449,7 @@
+   in_definition = FALSE;
+   while (! feof(V->f))
+     {
+-      getline(V);
++      getline_(V);
+       if (! feof(V->f) && strstr(V->sbuffer, "DEFINITION") == V->sbuffer)
+ 	{
+ 	  if ((sptr = strtok(V->sbuffer+12, "\n")) != NULL)
+@@ -482,11 +482,11 @@
+ 
+ 
+   while (!(feof(V->f) || ((*V->sbuffer!=0) && (strstr(V->sbuffer,"LOCUS") == V->sbuffer))))
+-    getline(V);
++    getline_(V);
+ 				/* SRE: V->s now holds "//", so sequential
+ 				   reads are wedged: fixed Tue Jul 13 1993 */
+   while (!feof(V->f) && strstr(V->sbuffer, "LOCUS  ") != V->sbuffer)
+-    getline(V);
++    getline_(V);
+ }
+ 
+ static int
+@@ -515,7 +515,7 @@
+     Die("bogus GCGdata format? %s", V->sbuffer);
+ 
+ 				/* second line contains free text description */
+-  getline(V);
++  getline_(V);
+   SetSeqinfoString(V->sqinfo, V->sbuffer, SQINFO_DESC);
+ 
+   if (binary) {
+@@ -535,7 +535,7 @@
+   else readLoop(0, endGCGdata, V);
+   
+   while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>'))))
+-    getline(V);
++    getline_(V);
+ }
+ 
+ static int
+@@ -555,12 +555,12 @@
+   if ((sptr = strtok(NULL, "\n")) != NULL)
+     SetSeqinfoString(V->sqinfo, sptr, SQINFO_DESC);
+ 				/* workaround for long NCBI NR lines */
+-  while (V->longline && ! feof(V->f)) getline(V);
++  while (V->longline && ! feof(V->f)) getline_(V);
+ 
+   readLoop(0, endPearson, V);
+ 
+   while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>'))))
+-    getline(V);
++    getline_(V);
+ }
+ 
+ 
+@@ -587,7 +587,7 @@
+ 
+ 				/* make sure we have first line */
+   while (!feof(V->f) && strncmp(V->sbuffer, "ID  ", 4) != 0)
+-    getline(V);
++    getline_(V);
+ 
+   if ((sptr = strtok(V->sbuffer+5, "\n\t ")) != NULL)
+     {
+@@ -596,7 +596,7 @@
+     }
+ 
+   do {
+-    getline(V);
++    getline_(V);
+     if (!feof(V->f) && strstr(V->sbuffer, "AC  ") == V->sbuffer)
+       {
+ 	if ((sptr = strtok(V->sbuffer+5, ";  \t\n")) != NULL)
+@@ -620,7 +620,7 @@
+ 
+ 				/* load next record's ID line */
+   while (!feof(V->f) && strncmp(V->sbuffer, "ID  ", 4) != 0)
+-    getline(V);
++    getline_(V);
+ }
+ 
+ 
+@@ -636,7 +636,7 @@
+ {
+   char *sptr;
+ 
+-  getline(V);  /*s == "seqLen seqid string..."*/
++  getline_(V);  /*s == "seqLen seqid string..."*/
+ 
+   if ((sptr = strtok(V->sbuffer+6, " \t\n")) != NULL)
+     SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME);
+@@ -647,7 +647,7 @@
+   readLoop(0, endZuker, V);
+ 
+   while (!(feof(V->f) | ((*V->sbuffer != '\0') & (*V->sbuffer == '('))))
+-    getline(V);
++    getline_(V);
+ }
+ 
+ static void 
+@@ -669,7 +669,7 @@
+ 
+   do {
+     done = feof(V->f);
+-    getline(V);
++    getline_(V);
+     if (! done) addseq(V->sbuffer, V);
+   } while (!done);
+ }
+@@ -681,7 +681,7 @@
+   char *sptr;
+   int   dostruc = FALSE;
+ 
+-  while (strncmp(V->sbuffer, "NAM ", 4) != 0) getline(V);
++  while (strncmp(V->sbuffer, "NAM ", 4) != 0) getline_(V);
+ 
+   if ((sptr = strtok(V->sbuffer+4, "\n\t ")) != NULL)
+     SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME);
+@@ -689,7 +689,7 @@
+   /*CONSTCOND*/
+   while (1)
+     {
+-      getline(V);
++      getline_(V);
+       if (feof(V->f)) {squid_errno = SQERR_FORMAT; return; }
+ 
+       if (strncmp(V->sbuffer, "SRC ", 4) == 0)
+@@ -721,14 +721,14 @@
+   while (1)
+     {
+ 				/* sequence line */
+-      getline(V);
++      getline_(V);
+       if (feof(V->f) || strncmp(V->sbuffer, "++", 2) == 0) 
+ 	break;
+       addseq(V->sbuffer, V);
+ 				/* structure line */
+       if (dostruc)
+ 	{
+-	  getline(V);
++	  getline_(V);
+ 	  if (feof(V->f)) { squid_errno = SQERR_FORMAT; return; }
+ 	  addstruc(V->sbuffer, V);
+ 	}
+@@ -736,7 +736,7 @@
+ 
+ 
+   while (!feof(V->f) && strncmp(V->sbuffer, "NAM ", 4) != 0)
+-    getline(V);
++    getline_(V);
+ }
+ 
+ 
+@@ -816,7 +816,7 @@
+ 
+   /* Load the first line.
+    */
+-  getline(dbfp);
++  getline_(dbfp);
+ 
+   return dbfp;
+ }
+@@ -833,7 +833,7 @@
+     Die("SeqfilePosition() failed: in a nonrewindable data file or stream");
+ 
+   fseek(sqfp->f, offset, SEEK_SET);
+-  getline(sqfp);
++  getline_(sqfp);
+ }
+ 
+ 
+@@ -853,7 +853,7 @@
+   if (sqfp->ali_aseqs != NULL) sqfp->ali_curridx = 0;
+   else {
+     rewind(sqfp->f);
+-    getline(sqfp);
++    getline_(sqfp);
+   }
+ }
+ 
+@@ -949,7 +949,7 @@
+       do {			/* skip leading comments on GCG file */
+ 	gotuw = (strstr(V->sbuffer,"..") != NULL);
+ 	if (gotuw) readUWGCG(V);
+-	getline(V);
++	getline_(V);
+       } while (! feof(V->f));
+       break;
+ 
--- wise-2.4.1.orig/debian/patches/03_doc-nodycache.patch
+++ wise-2.4.1/debian/patches/03_doc-nodycache.patch
@@ -0,0 +1,19 @@
+#! /bin/sh /usr/share/dpatch/dpatch-run
+## 03_doc-nodycache.dpatch by Philipp Benner <mail@philipp-benner.de>
+##
+## DP: Documentation bugfix.
+
+@DPATCH@
+diff -urNad wise-2.4.0~/docs/wise2.tex wise-2.4.0/docs/wise2.tex
+--- wise-2.4.0~/docs/wise2.tex	2003-03-26 12:47:08.000000000 +0100
++++ wise-2.4.0/docs/wise2.tex	2007-07-16 01:05:34.000000000 +0200
+@@ -1617,7 +1617,8 @@
+ \item[-hithelp]   more detailed help on hitlist formats
+ \item[-dymem]      memory style [default/linear/explicit]
+ \item[-kbyte]       memory amount to use [4000]
+-\item[-\[no\]dycache] implicitly cache dy matrix usage (default yes)
++\item[-dycache] implicitly cache dy matrix usage (default)
++\item[-nodycache] do not implicitly cache dy matrix usage
+ \item[-dydebug]     drop into dynamite dp matrix debugger
+ \item[-paldebug]    print PackAln after debugger run if used
+ \item[-help]      show help options
--- wise-2.4.1.orig/debian/patches/04_wise2-pdflatex-update.patch
+++ wise-2.4.1/debian/patches/04_wise2-pdflatex-update.patch
@@ -0,0 +1,43 @@
+#! /bin/sh /usr/share/dpatch/dpatch-run
+## 04_wise2-pdflatex-update.dpatch by Philipp Benner <mail@philipp-benner.de>
+##
+## DP: Make wise2.tex pdflatex compatible.
+
+@DPATCH@
+
+diff -urNad wise-2.4.0~/docs/wise2.tex wise-2.4.0/docs/wise2.tex
+--- wise-2.4.0~/docs/wise2.tex	2007-08-06 10:25:05.000000000 +0200
++++ wise-2.4.0/docs/wise2.tex	2007-08-06 10:25:08.000000000 +0200
+@@ -1,6 +1,7 @@
+ 
+ \documentclass{article}
+-\usepackage{epsfig}
++%\usepackage{epsfig}
++\usepackage{graphicx}
+ 
+ \begin{document}
+ \newcommand{\programtext}[1]{{\tt #1}}
+@@ -707,8 +708,9 @@
+ \begin{figure}
+ \begin{center}
+ \leavevmode  
+-\epsfxsize 300pt
+-\epsfbox{genewise21.eps}
++%\epsfxsize 300pt
++%\epsfbox{genewise21.eps}
++%\includegraphics[scale=0.75]{genewise21.pdf}
+ \newline     
+ \caption{GeneWise21:93 Algorithm. The dark circles represent states, and the
+ arrows between them transitions. Black transitions are standard
+@@ -898,8 +900,9 @@
+ \begin{figure}
+ \begin{center}
+ \leavevmode  
+-\epsfxsize 300pt
+-\epsfbox{genewise6.eps}
++%\epsfxsize 300pt
++%\epsfbox{genewise6.eps}
++%\includegraphics[scale=0.75]{genewise6.pdf}
+ \newline     
+ \caption{GeneWise6:23}
+ \label{Figure:genewise623}
--- wise-2.4.1.orig/debian/patches/05_glib2.patch
+++ wise-2.4.1/debian/patches/05_glib2.patch
@@ -0,0 +1,304 @@
+Author: Barry deFreese <bdefreese@debian.org>
+Description: To build wise2 with the Glib version 2.0 instead of 1.2.
+Forwarded: birney@sanger.ac.uk
+Index: wise-2.4.1/src/makefile
+===================================================================
+--- wise-2.4.1.orig/src/makefile	2011-09-12 14:48:39.377788497 +0000
++++ wise-2.4.1/src/makefile	2011-09-12 14:48:43.417793671 +0000
+@@ -31,13 +31,13 @@
+ 
+ 
+ # Intel icc flags
+-# CFLAGS = -c  -O3 -axWK -ipo `glib-config --cflags`
++# CFLAGS = -c  -O3 -axWK -ipo `pkg-config --cflags glib-2.0`
+ 
+ # alpha flags (-pthread)
+-# CFLAGS = -c -O3 -pthread `glib-config --cflags`
++# CFLAGS = -c -O3 -pthread `pkg-config --cflags glib-2.0`
+ 
+ # normal linux/bsd/mac flags
+-CFLAGS = -c -O3  `glib-config --cflags`
++CFLAGS = -c -O3  `pkg-config --cflags glib-2.0`
+ 
+ 
+ EXTRALIBS = -lm
+Index: wise-2.4.1/src/snp/makefile
+===================================================================
+--- wise-2.4.1.orig/src/snp/makefile	2005-05-02 21:07:09.000000000 +0000
++++ wise-2.4.1/src/snp/makefile	2011-09-12 14:48:43.417793671 +0000
+@@ -5,9 +5,9 @@
+ CC = cc
+ #CFLAGS = -c -O2  -pg -I../base/ -I../dynlibsrc/
+ #CFLAGS = -c -O2 -DPTHREAD -DHAS_PTHREAD_SETSCOPE  -DUNIX  -I../base/ -I../dynlibsrc/ -I.
+-CFLAGS = -c -g3 -O2  -DUNIX  -I../base/ -I../dynlibsrc/ -I. -pthread `glib-config --cflags`
++CFLAGS = -c -g3 -O2  -DUNIX  -I../base/ -I../dynlibsrc/ -I. -pthread `pkg-config --cflags glib-2.0`
+ 
+-LFLAGS =  -g -L../base/ -L../dynlibsrc/ -lpthread `glib-config --libs` -lpthread -lm
++LFLAGS =  -g -L../base/ -L../dynlibsrc/ -lpthread `pkg-config --libs glib-2.0` -lpthread -lm
+ AR_OPTIONS = ru
+ 
+ RANLIB_NEEDED = 0
+Index: wise-2.4.1/src/corba/makefile
+===================================================================
+--- wise-2.4.1.orig/src/corba/makefile	2005-08-23 12:58:43.000000000 +0000
++++ wise-2.4.1/src/corba/makefile	2011-09-12 14:48:43.417793671 +0000
+@@ -3,7 +3,7 @@
+ CC = cc
+ INCFLAGS = -I../base/ -I../dynlibsrc
+ #gCFLAGS = -Wall -g -pedantic -c  -DUNIX -I../base/
+-#CFLAGS =  -O2 -c  -DUNIX  -I../base/ `glib-config --cflags` -I/usr/local/include/orbit-1.0/
++#CFLAGS =  -O2 -c  -DUNIX  -I../base/ `pkg-config --cflags glib-2.0` -I/usr/local/include/orbit-1.0/
+ CFLAGS =  -pthread -c  -DUNIX  -I../base/ -I../dynlibsrc `orbit-config --cflags client`
+ LFLAGS =   -L../base/ -lm -lpthread
+ AR_OPTIONS = ru
+@@ -14,18 +14,18 @@
+ 	orbit-idl hspscan_corba.idl
+ 
+ test_server : test_server.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o 
+-	cc -g -o test_server  test_server.o hspscan_server_impl.o  hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o  corba_singleton.o ../dynlibsrc/libdyna.a ../base/libwisebase.a ../dynlibsrc/hsp.o ../dynlibsrc/subseqhash.o ../dynlibsrc/linkedlist_lookpos.o   ../dynlibsrc/libdyna_glib.a `glib-config --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread
++	cc -g -o test_server  test_server.o hspscan_server_impl.o  hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o  corba_singleton.o ../dynlibsrc/libdyna.a ../base/libwisebase.a ../dynlibsrc/hsp.o ../dynlibsrc/subseqhash.o ../dynlibsrc/linkedlist_lookpos.o   ../dynlibsrc/libdyna_glib.a `pkg-config --libs glib-2.0` -lm -lORBit -lIIOP -lORBitutil -lpthread
+ 
+ scanwise_protein_index : scanwise_protein_index.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o 
+-	cc -o scanwise_protein_index  scanwise_protein_index.o hspscan_server_impl.o  hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o  corba_singleton.o  ../dynlibsrc/libdyna_glib.a ../dynlibsrc/libdyna.a ../base/libwisebase.a `glib-config --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread
++	cc -o scanwise_protein_index  scanwise_protein_index.o hspscan_server_impl.o  hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o  corba_singleton.o  ../dynlibsrc/libdyna_glib.a ../dynlibsrc/libdyna.a ../base/libwisebase.a `pkg-config --libs glib-2.0` -lm -lORBit -lIIOP -lORBitutil -lpthread
+ 
+ 
+ test_client : test_client.o hspscan_corba-common.o hspscan_corba-stubs.o 
+-	cc -g -o test_client  test_client.o  hspscan_corba-common.o hspscan_corba-stubs.o ../dynlibsrc/libdyna.a ../base/libwisebase.a `glib-config --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread
++	cc -g -o test_client  test_client.o  hspscan_corba-common.o hspscan_corba-stubs.o ../dynlibsrc/libdyna.a ../base/libwisebase.a `pkg-config --libs glib-2.0` -lm -lORBit -lIIOP -lORBitutil -lpthread
+ 
+ 
+ test_wrapper : test_wrapper.o hspscan_corba-common.o hspscan_corba-stubs.o hspscan_corba_wrapper.o corba_singleton.o 
+-	cc -g -o test_wrapper test_wrapper.o  hspscan_corba-common.o hspscan_corba-stubs.o   corba_singleton.o hspscan_corba_wrapper.o ../dynlibsrc/hsp.o ../dynlibsrc/libdyna.a ../base/libwisebase.a  `glib-config --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread
++	cc -g -o test_wrapper test_wrapper.o  hspscan_corba-common.o hspscan_corba-stubs.o   corba_singleton.o hspscan_corba_wrapper.o ../dynlibsrc/hsp.o ../dynlibsrc/libdyna.a ../base/libwisebase.a  `pkg-config --libs glib-2.0` -lm -lORBit -lIIOP -lORBitutil -lpthread
+ 
+ .c.o :
+ 	$(CC) $(CFLAGS) $(INCFLAGS) $?
+Index: wise-2.4.1/src/models/makefile
+===================================================================
+--- wise-2.4.1.orig/src/models/makefile	2006-04-17 08:28:12.000000000 +0000
++++ wise-2.4.1/src/models/makefile	2011-09-12 14:45:45.507532441 +0000
+@@ -192,10 +192,10 @@
+ 	$(CC) -o psw psw.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o   $(LFLAGS) -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
+ 
+ scanwisep.o : scanwisep.c
+-	$(CC) $(CFLAGS) $(INCFLAGS) -I../external/mott `glib-config --cflags` $?
++	$(CC) $(CFLAGS) $(INCFLAGS) -I../external/mott `pkg-config --cflags glib-2.0` $?
+ 
+ hsp2aln_sw.o : hsp2aln_sw.c
+-	$(CC) $(CFLAGS) $(INCFLAGS) `glib-config --cflags` $?
++	$(CC) $(CFLAGS) $(INCFLAGS) `pkg-config --cflags glib-2.0` $?
+ 
+ scanwisep_mysql.o : scanwisep.c
+ 	$(CC)  $(CFLAGS) -DSCAN_MYSQL -I../corba -I../external/mott -I../mysql/protein_index/ -I/usr/local/mysql/include scanwisep.c 
+@@ -215,7 +215,7 @@
+ 	$(CC)  $(CFLAGS) $(INCFLAGS)  -o scanwisep_wiseserver.o -DSCAN_WISESERVER -I../network -I../socket -I../external/mott scanwisep.c 
+ 
+ scanwise : scanwisep_wiseserver.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o hsp2aln_sw.o
+-	$(CC) -o scanwise scanwisep_wiseserver.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o   ../network/net_hspscan.o ../network/client_multihspscan.o  $(LFLAGS) -L../external/mott -L../socket -lmott -ldyna_glib -ldyna -lwisesocket -lwisebase  $(EXTRALIBS) -lpthread 
++	$(CC) -o scanwise scanwisep_wiseserver.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o   ../network/net_hspscan.o ../network/client_multihspscan.o  $(LFLAGS) -L../external/mott -L../socket -lmott -ldyna_glib -ldyna -lwisesocket -lwisebase  $(EXTRALIBS) -lpthread $(LFLAGS)
+ 
+ scanwisep_compress.o : scanwisep.c
+ 	$(CC)  $(CFLAGS) -DSCAN_COMPRESS -I../dnaindex -I../network -I../socket -I../external/mott scanwisep.c 
+@@ -226,25 +226,25 @@
+ 
+ 
+ scanwisep : scanwisep.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o hsp2aln_sw.o
+-	$(CC) -o scanwisep scanwisep.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o   $(LFLAGS)  -L../external/mott -lmott -ldyna_glib -ldyna  -lwisebase  $(EXTRALIBS) `glib-config --libs` -lpthread
++	$(CC) -o scanwisep scanwisep.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o   $(LFLAGS)  -L../external/mott -lmott -ldyna_glib -ldyna  -lwisebase  $(EXTRALIBS) `pkg-config --libs glib-2.0` -lpthread
+ 
+ test_gwhsp : test_gwhsp.o genewisehsp.o
+-	$(CC) -o test_gwhsp test_gwhsp.o genewisehsp.o $(LFLAGS) -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS) `glib-config --libs` -lpthread
++	$(CC) -o test_gwhsp test_gwhsp.o genewisehsp.o $(LFLAGS) -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS) `pkg-config --libs glib-2.0` -lpthread
+ 
+ localcishit.o : localcishit.c
+-	$(CC) $(CFLAGS) $(INCFLAGS) `glib-config --cflags` $?
++	$(CC) $(CFLAGS) $(INCFLAGS) `pkg-config --cflags glib-2.0` $?
+ 
+ promoterwise.o : promoterwise.c  
+-	$(CC) $(CFLAGS) $(INCFLAGS) `glib-config --cflags` $?
++	$(CC) $(CFLAGS) $(INCFLAGS) `pkg-config --cflags glib-2.0` $?
+ 
+ promoterwise : promoterwise.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o
+-	$(CC) -g -o promoterwise promoterwise.o localdba.o  localcishit.o localcispara.o dbadisplay.o  motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o  pairwiseshortdna.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS) `glib-config --libs` -lpthread
++	$(CC) -g -o promoterwise promoterwise.o localdba.o  localcishit.o localcispara.o dbadisplay.o  motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o  pairwiseshortdna.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS) `pkg-config --libs glib-2.0` -lpthread
+ 
+ test_deng : test_deng.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o
+-	$(CC) -o test_deng test_deng.o  localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS) `glib-config --libs` -lpthread
++	$(CC) -o test_deng test_deng.o  localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS) `pkg-config --libs glib-2.0` -lpthread
+ 
+ promotercluster : promotercluster.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o
+-	$(CC) -o promotercluster promotercluster.o  localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS) `glib-config --libs` -lpthread
++	$(CC) -o promotercluster promotercluster.o  localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS) `pkg-config --libs glib-2.0` -lpthread
+ 
+ dnawise : dnawise.o dnahmm.o dnahmmdp.o seqaligndisplay.o 
+ 	$(CC) -o dnawise dnawise.o dnahmm.o dnahmmdp.o  seqaligndisplay.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase  -lpthread
+@@ -275,7 +275,7 @@
+ 	$(CC) -o makerandomdb makerandomdb.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
+ 
+ genewise : genewise.o $(NEWG) 
+-	$(CC) -o genewise genewise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
++	$(CC) -o genewise genewise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS) $(LFLAGS)
+ 
+ cdnawise : cdnawise.o $(NEWG) cdnawise10.o 
+ 	$(CC) -g -o cdnawise cdnawise.o cdnawise10.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
+@@ -300,16 +300,16 @@
+ 
+ 
+ genewisedb : genewisedb.o $(NEWG) 
+-	$(CC) -g -o genewisedb genewisedb.o  $(NEWG)  $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS) 
++	$(CC) -g -o genewisedb genewisedb.o  $(NEWG)  $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)  $(LFLAGS)
+ 
+ estwisedb : estwisedb.o $(NEWG) 
+-	$(CC) -g -o estwisedb estwisedb.o $(NEWG)  $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
++	$(CC) -g -o estwisedb estwisedb.o $(NEWG)  $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS) $(LFLAGS)
+ 
+ edb : estwisedb.o $(NEWG) 
+ 	$(CC) -g -o estwisedb estwisedb.o $(NEWG)  $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS) -lefence
+ 
+ estwise : estwise.o $(NEWG) 
+-	$(CC) -g -o estwise estwise.o  $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
++	$(CC) -g -o estwise estwise.o  $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS) $(LFLAGS)
+ 
+ 
+ amplimer_resolver : amplimer_resolver.o dnaalign.o dnamatcher.o 
+@@ -331,7 +331,7 @@
+ 	$(CC) -g -o statwise statwise.o statwise10.o syexonmodel.o genestats.o pwmdna.o geneutil.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
+ 
+ pseudowise : pseudowise.o pseudowise7.o $(NEWG) 
+-	$(CC) -g -o pseudowise pseudowise.o pseudowise7.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
++	$(CC) -g -o pseudowise pseudowise.o pseudowise7.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS) $(LFLAGS)
+ 
+ clonewise : clonewise.o clonewisedp.o localclonewisedp.o mapstruct.o
+ 	$(CC) -g -o clonewise clonewise.o clonewisedp.o localclonewisedp.o mapstruct.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
+@@ -345,11 +345,11 @@
+ CC = cc
+ #CFLAGS = -c -O2  -pg -I../base/ -I../dynlibsrc/
+ #CFLAGS = -c -O2 -DPTHREAD -DHAS_PTHREAD_SETSCOPE  -DUNIX  -I../base/ -I../dynlibsrc/ -I.
+-CFLAGS = -c -g3 -O2  -DUNIX  -I../base/ -I../dynlibsrc/ -I. -pthread `glib-config --cflags`
+-#CFLAGS = -c  -g -DHAS_PTHREAD_SETSCOPE -DUNIX -I../base/ -I../dynlibsrc/ `glib-config --cflags`
++CFLAGS = -c -g3 -O2  -DUNIX  -I../base/ -I../dynlibsrc/ -I. -pthread `pkg-config --cflags glib-2.0`
++#CFLAGS = -c  -g -DHAS_PTHREAD_SETSCOPE -DUNIX -I../base/ -I../dynlibsrc/ `pkg-config --cflags glib-2.0`
+ #LFLAGS =  -L../base/ -L../dynlibsrc/ -L../HMMer2/  
+ 
+-LFLAGS =  -L../base/ -L../dynlibsrc/ -L$(HMMER_LIBS) -lpthread `glib-config --libs`
++LFLAGS =  -L../base/ -L../dynlibsrc/ -L$(HMMER_LIBS) -lpthread `pkg-config --libs glib-2.0`
+ AR_OPTIONS = ru
+ 
+ RANLIB_NEEDED = 0
+Index: wise-2.4.1/src/dnaindex/makefile
+===================================================================
+--- wise-2.4.1.orig/src/dnaindex/makefile	2005-12-06 09:43:19.000000000 +0000
++++ wise-2.4.1/src/dnaindex/makefile	2011-09-12 14:48:43.427793574 +0000
+@@ -27,14 +27,14 @@
+ 
+ 
+ kwise : kwise.o $(ASSEMBLY_OBJ)
+-	$(CC) -o kwise kwise.o $(ASSEMBLY_OBJ)  -ldyna -lwisebase $(LFLAGS) `glib-config --libs`
++	$(CC) -o kwise kwise.o $(ASSEMBLY_OBJ)  -ldyna -lwisebase $(LFLAGS) `pkg-config --libs glib-2.0`
+ 
+ arraymatcher : arraymatcher.o $(ASSEMBLY_OBJ) 
+-	$(CC) -o arraymatcher arraymatcher.o $(ASSEMBLY_OBJ)  -ldyna -lwisebase $(LFLAGS) `glib-config --libs`
++	$(CC) -o arraymatcher arraymatcher.o $(ASSEMBLY_OBJ)  -ldyna -lwisebase $(LFLAGS) `pkg-config --libs glib-2.0`
+ 
+ 
+ findbad_kmer : findbad_kmer.o $(ASSEMBLY_OBJ)
+-	$(CC) -o findbad_kmer findbad_kmer.o $(ASSEMBLY_OBJ)  -ldyna -lwisebase $(LFLAGS) `glib-config --libs`
++	$(CC) -o findbad_kmer findbad_kmer.o $(ASSEMBLY_OBJ)  -ldyna -lwisebase $(LFLAGS) `pkg-config --libs glib-2.0`
+ 
+ make_shotgun : make_shotgun.o shotgun.o
+ 	$(CC) -o make_shotgun make_shotgun.o shotgun.o -ldyna -lwisebase $(LFLAGS)
+@@ -70,10 +70,10 @@
+ 	$(CC) -o show_euler show_euler.o eulerindex.o singleseqspace.o -ldyna -lwisebase $(LFLAGS)
+ 
+ CC = cc
+-CFLAGS = -pthread -c  -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../base/ -I../dynlibsrc/ `glib-config --cflags`
++CFLAGS = -pthread -c  -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../base/ -I../dynlibsrc/ `pkg-config --cflags glib-2.0`
+ 
+ 
+-LFLAGS =  -g -L../base/ -L../dynlibsrc/ -lpthread `glib-config --libs` -lm
++LFLAGS =  -g -L../base/ -L../dynlibsrc/ -lpthread `pkg-config --libs glib-2.0` -lm
+ 
+ 
+ .c.o :
+Index: wise-2.4.1/src/dnaindex/assembly/makefile
+===================================================================
+--- wise-2.4.1.orig/src/dnaindex/assembly/makefile	2005-02-23 11:46:22.000000000 +0000
++++ wise-2.4.1/src/dnaindex/assembly/makefile	2011-09-12 14:48:43.427793574 +0000
+@@ -26,10 +26,10 @@
+ 
+ 
+ CC = cc
+-CFLAGS = -Wall -pthread -c  -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../../base/ -I../../dynlibsrc/ -I../ -I../../models/ `glib-config --cflags`
++CFLAGS = -Wall -pthread -c  -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../../base/ -I../../dynlibsrc/ -I../ -I../../models/ `pkg-config --cflags glib-2.0`
+ 
+ 
+-LFLAGS =  -g -L../../base/ -L../../dynlibsrc/ -lpthread `glib-config --libs` -lm
++LFLAGS =  -g -L../../base/ -L../../dynlibsrc/ -lpthread `pkg-config --libs glib-2.0` -lm
+ 
+ 
+ .c.o :
+Index: wise-2.4.1/src/dynlibsrc/makefile
+===================================================================
+--- wise-2.4.1.orig/src/dynlibsrc/makefile	2006-04-19 11:48:31.000000000 +0000
++++ wise-2.4.1/src/dynlibsrc/makefile	2011-09-12 14:48:43.427793574 +0000
+@@ -84,9 +84,9 @@
+ CC = cc
+ INCFLAGS = -I../base/
+ #CFLAGS = -Wall -g -pedantic -c  -DUNIX -I../base/
+-CFLAGS =  -Wall -pthread -g3 -DCOMPILE_VERBOSITY -DPTHREAD -O2 -c  -DUNIX -I../base/ `glib-config --cflags`
+-#CFLAGS =  -Wall -g3 -pg -DPTHREAD -O2  -c  -DUNIX -I../base/ `glib-config --cflags`
+-#CFLAGS =   -O2 -c -pthread  -DUNIX  -I../base/ `glib-config --cflags`
++CFLAGS =  -Wall -pthread -g3 -DCOMPILE_VERBOSITY -DPTHREAD -O2 -c  -DUNIX -I../base/ `pkg-config --cflags glib-2.0`
++#CFLAGS =  -Wall -g3 -pg -DPTHREAD -O2  -c  -DUNIX -I../base/ `pkg-config --cflags glib-2.0`
++#CFLAGS =   -O2 -c -pthread  -DUNIX  -I../base/ `pkg-config --cflags glib-2.0`
+ #CFLAGS =   -O -c -DUNIX -DNOERROR -I../base/
+ LFLAGS =  -g -L../base/ -lm 
+ AR_OPTIONS = ru
+@@ -148,13 +148,13 @@
+ 	$(CC) -g -o test_shadowindex test_shadowindex.o shadowseqindex.o shadowseq.o ./libdyna.a ../base/libwisebase.a -lm
+ 
+ test_seqhash : test_seqhash.o subseqhash.o hsp.o hitlist.o hspscaninterface.o hsplookupscan.o libdyna.a
+-	$(CC) -g -o test_seqhash `glib-config --libs` test_seqhash.o subseqhash.o hsp.o  hitlist.o hspscaninterface.o hsplookupscan.o libdyna.a ../base/libwisebase.a -lm  
++	$(CC) -g -o test_seqhash `pkg-config --libs glib-2.0` test_seqhash.o subseqhash.o hsp.o  hitlist.o hspscaninterface.o hsplookupscan.o libdyna.a ../base/libwisebase.a -lm  
+ 
+ test_hsp : test_hsp.o codon.o sequence.o hsp.o compmat.o probability.o 
+-	$(CC) -g -o test_hsp test_hsp.o codon.o sequence.o hsp.o compmat.o probability.o  ../base/libwisebase.a -lm `glib-config --libs`
++	$(CC) -g -o test_hsp test_hsp.o codon.o sequence.o hsp.o compmat.o probability.o  ../base/libwisebase.a -lm `pkg-config --libs glib-2.0`
+ 
+ test_topscore : test_topscore.o codon.o sequence.o hsp.o compmat.o probability.o 
+-	$(CC) -g -o test_topscore test_topscore.o codon.o sequence.o hsp.o compmat.o probability.o  ../base/libwisebase.a -lm `glib-config --libs`
++	$(CC) -g -o test_topscore test_topscore.o codon.o sequence.o hsp.o compmat.o probability.o  ../base/libwisebase.a -lm `pkg-config --libs glib-2.0`
+ 
+ 
+ testgendb : probability.o genomicdb.o genomic.o testgendb.o sequence.o codon.o sequencedb.o complexsequence.o complexevalset.o
+Index: wise-2.4.1/src/network/makefile
+===================================================================
+--- wise-2.4.1.orig/src/network/makefile	2006-04-19 16:39:46.000000000 +0000
++++ wise-2.4.1/src/network/makefile	2011-09-12 14:48:43.427793574 +0000
+@@ -3,8 +3,8 @@
+ 
+ CC = cc
+ INCFLAGS = -I../base/  -I../socket -I../dynlibsrc -I../dnaindex
+-CFLAGS =    -O2  -c -pthread  -DUNIX  -I../base/ -I../socket -I../dynlibsrc -I../dnaindex `glib-config --cflags`
+-LFLAGS =  -g -L../base/ -L../socket -L../dynlibsrc -L../dnaindex -lm `glib-config --libs`
++CFLAGS =    -O2  -c -pthread  -DUNIX  -I../base/ -I../socket -I../dynlibsrc -I../dnaindex `pkg-config --cflags glib-2.0`
++LFLAGS =  -g -L../base/ -L../socket -L../dynlibsrc -L../dnaindex -lm `pkg-config --libs glib-2.0`
+ AR_OPTIONS = ru
+ 
+ RANLIB_NEEDED = 0
+Index: wise-2.4.1/src/other_programs/makefile
+===================================================================
+--- wise-2.4.1.orig/src/other_programs/makefile	2005-10-25 06:27:46.000000000 +0000
++++ wise-2.4.1/src/other_programs/makefile	2011-09-12 14:48:43.427793574 +0000
+@@ -3,8 +3,8 @@
+ .SUFFIXES :  .dy
+ 
+ CC = cc
+-CFLAGS =   -O2 -g3 -c -pthread  -DUNIX  -I../base/ -I../dynlibsrc `glib-config --cflags`
+-LFLAGS =  -g -L../base/ -L../dynlibsrc  -lm `glib-config --libs`
++CFLAGS =   -O2 -g3 -c -pthread  -DUNIX  -I../base/ -I../dynlibsrc `pkg-config --cflags glib-2.0`
++LFLAGS =  -g -L../base/ -L../dynlibsrc  -lm `pkg-config --libs glib-2.0`
+ AR_OPTIONS = ru
+ 
+ RANLIB_NEEDED = 0
--- wise-2.4.1.orig/debian/patches/series
+++ wise-2.4.1/debian/patches/series
@@ -0,0 +1,6 @@
+01_welcome-csh.patch
+02_isnumber.patch
+03_doc-nodycache.patch
+04_wise2-pdflatex-update.patch
+05_glib2.patch
+06_getline.patch
--- wise-2.4.1.orig/debian/patches/01_welcome-csh.patch
+++ wise-2.4.1/debian/patches/01_welcome-csh.patch
@@ -0,0 +1,28 @@
+#! /bin/sh /usr/share/dpatch/dpatch-run
+## 01_welcome-csh.dpatch by Philipp Benner <mail@philipp-benner.de>
+##
+## All lines beginning with `## DP:' are a description of the patch.
+## DP: No description.
+
+@DPATCH@
+diff -urNad wise-2.4.0~/src/makefile wise-2.4.0/src/makefile
+--- wise-2.4.0~/src/makefile	2007-07-15 23:39:24.000000000 +0200
++++ wise-2.4.0/src/makefile	2007-07-15 23:41:11.000000000 +0200
+@@ -109,7 +109,7 @@
+ bin : 
+ 	mkdir bin
+ 	cp models/pswdb models/psw models/genewisedb models/estwisedb models/estwise models/genewise models/dba models/dnal models/promoterwise network/scanwise_server models/scanwise ./bin
+-	csh welcome.csh
++	./welcome.csh
+ 
+ libs : 
+ 	(cd base   ; $(MAKE) CC="$(CC)" CFLAGS="$(CFLAGS)" libwisebase.a )
+diff -urNad wise-2.4.0~/src/welcome.csh wise-2.4.0/src/welcome.csh
+--- wise-2.4.0~/src/welcome.csh	2007-07-15 23:39:24.000000000 +0200
++++ wise-2.4.0/src/welcome.csh	2007-07-15 23:40:46.000000000 +0200
+@@ -1,4 +1,4 @@
+-#!/bin/tcsh -f
++#!/bin/sh
+ 
+ echo ""
+ echo "Welcome to Wise2.4"