dialign-t (1.0.2-1) debian-dir only changes

Summary

 debian/README.Debian           |   13 +
 debian/changelog               |   51 +++++
 debian/compat                  |    1 
 debian/control                 |   41 ++++
 debian/copyright               |   32 +++
 debian/dialign-tx-data.install |    2 
 debian/dialign-tx.1            |  266 ++++++++++++++++++++++++++
 debian/dialign-tx.1.xml        |  413 +++++++++++++++++++++++++++++++++++++++++
 debian/dialign-tx.install      |    1 
 debian/dialign-tx.manpages     |    1 
 debian/rules                   |    9 
 debian/watch                   |    3 
 12 files changed, 833 insertions(+)

    
download this patch

Patch contents

--- dialign-t-1.0.2.orig/debian/watch
+++ dialign-t-1.0.2/debian/watch
@@ -0,0 +1,3 @@
+version=3
+#opts="dversionmangle=s/.dfsg.*//" \
+http://dialign-tx.gobics.de/download http://dialign-tx.gobics.de/DIALIGN-TX_(.*)\.tar\.gz
--- dialign-t-1.0.2.orig/debian/dialign-tx-data.install
+++ dialign-t-1.0.2/debian/dialign-tx-data.install
@@ -0,0 +1,2 @@
+conf/*			usr/share/dialign-tx/
+data/*			usr/share/dialign-tx/
--- dialign-t-1.0.2.orig/debian/dialign-tx.manpages
+++ dialign-t-1.0.2/debian/dialign-tx.manpages
@@ -0,0 +1 @@
+debian/dialign-tx.1
--- dialign-t-1.0.2.orig/debian/README.Debian
+++ dialign-t-1.0.2/debian/README.Debian
@@ -0,0 +1,13 @@
+DIALIGN-TX for Debian
+--------------------
+
+The configuration directory shipped with the source is installed in
+/usr/share/dialign-tx on your system.
+
+
+Possible issues with this package:
+
+ - Users have no write acces to /usr/share/dialign-tx, so problems are expected
+   when running dialign-t -C.
+
+ -- Charles Plessy <plessy@debian.org>  Fri, 04 Apr 2008 11:23:25 +0900
--- dialign-t-1.0.2.orig/debian/rules
+++ dialign-t-1.0.2/debian/rules
@@ -0,0 +1,9 @@
+#!/usr/bin/make -f
+
+include /usr/share/cdbs/1/rules/debhelper.mk
+include /usr/share/cdbs/1/class/makefile.mk
+
+DEB_SRCDIR 		= $(CURDIR)/source
+
+binary-fixup/dialign-tx-data::
+	chmod 644 $(CURDIR)/debian/dialign-tx-data/usr/share/dialign-tx/*
--- dialign-t-1.0.2.orig/debian/control
+++ dialign-t-1.0.2/debian/control
@@ -0,0 +1,41 @@
+Source: dialign-t
+Section: science
+Priority: optional
+Maintainer: Debian-Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Charles Plessy <plessy@debian.org>
+Build-Depends: debhelper (>= 7), cdbs
+Standards-Version: 3.8.0
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/dialign-t/trunk/?rev=0&sc=0
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/dialign-t/trunk/
+Homepage: http://dialign-tx.gobics.de/
+
+Package: dialign-tx
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}, dialign-tx-data (= ${source:Version})
+Conflicts: dialign-t, dialign-t-doc
+Replaces: dialign-t, dialign-t-doc
+Provides: dialign-t, dialign-t-doc
+Enhances: t-coffee
+Description: Segment-based multiple sequence alignment
+ DIALIGN-TX is a command line tool to perform multiple alignment of protein or
+ DNA sequences. It is a complete reimplementation of the segment-base approach
+ including several new improvements and heuristics that significantly enhance
+ the quality of the output alignments compared to DIALIGN 2.2 and DIALIGN-T.
+ For pairwise alignment, DIALIGN-TX uses a fragment-chaining algorithm that
+ favours chains of low-scoring local alignments over isolated high-scoring
+ fragments. For multiple alignment, DIALIGN-TX uses an improved greedy
+ procedure that is less sensitive to spurious local sequence similarities.
+ .
+ DIALIGN-TX has been published in Amarendran R. Subramanian, Michael Kaufmann,
+ Burkhard Morgenstern: Improvement of the segment-based approach for multiple
+ sequence alignment by combining greedy and progressive alignment strategies,
+ Algorithms for Molecular Biology 3:6, 2008
+
+Package: dialign-tx-data
+Architecture: all
+Depends: ${misc:Depends}
+Recommends: dialign-tx (= ${binary:Version})
+Description: Common data files for dialign-tx
+ This package contain the score matrices and probability distribution files
+ that DIALIGN-TX needs to align peptidic and nucleic sequences.
--- dialign-t-1.0.2.orig/debian/dialign-tx.1.xml
+++ dialign-t-1.0.2/debian/dialign-tx.1.xml
@@ -0,0 +1,413 @@
+<?xml version='1.0' encoding='ISO-8859-1'?>
+<?xml-stylesheet type="text/xsl"
+	href="http://docbook.sourceforge.net/release/xsl/current/manpages/docbook.xsl"?>
+<!DOCTYPE refentry PUBLIC "-//OASIS//DTD DocBook XML V4.5//EN"
+	"http://www.oasis-open.org/docbook/xml/4.5/docbookx.dtd" [
+
+<!-- Process this file with an XSLT processor, e.g. xsltproc:    -->
+<!-- `xsltproc \
+      -''-nonet \
+      -''-param man.charmap.use.subset "0" \
+      -''-param make.year.ranges "1" \
+      -''-param make.single.year.ranges "1" \
+      manpage.xml'                                               -->
+
+<!-- Template from docbook-xsl 1.73.2.dfsg.1-2 -->
+
+  <!ENTITY dhfirstname "Charles">
+  <!ENTITY dhsurname   "Plessy">
+  <!ENTITY dhemail     "plessy@debian.org">
+  <!ENTITY dhusername  "&dhfirstname; &dhsurname;">
+  <!ENTITY dhrelease   "1.0.2">
+  <!ENTITY dhtitle     "DIALIGN-TX: Parameters">
+  <!ENTITY dhucpackage "DIALIGN-TX">
+  <!ENTITY dhpackage   "dialign-tx">
+  <!ENTITY dhproduct   "&dhpackage;">
+  <!ENTITY dhsection   "1">
+  
+  <!ENTITY config-dir  "/usr/share/dialign-tx">
+]>
+
+<refentry>
+	<refentryinfo>
+		<title>&dhtitle;</title>
+		<productname>&dhpackage;</productname>
+		<releaseinfo role="version">&dhrelease;</releaseinfo>
+		<authorgroup>
+			<author>
+				<firstname>Amarendran R.</firstname>
+				<surname>Subramanian</surname>
+				<contrib>Author of &dhpackage;</contrib>
+				<address>
+					<email>subraman@informatik.uni-tuebingen.de</email>
+				</address>
+			</author>
+      
+      <author>
+				<firstname>Volker</firstname>
+				<surname>Menrad</surname>
+				<contrib>Co-author of &dhpackage;</contrib>
+			</author>
+      
+      <author>
+				<firstname>Dorothea</firstname>
+				<surname>Emig</surname>
+				<contrib>Co-author of &dhpackage;</contrib>
+			</author>
+    </authorgroup>
+    
+    <authorgroup>
+			<author>
+				<firstname>&dhfirstname;</firstname>
+				<surname>&dhsurname;</surname>
+				<contrib>Converted this guide in DocBook XML for the Debian distribution.</contrib>
+				<address>
+					<email>&dhemail;</email>
+				</address>
+			</author>
+		</authorgroup>
+    
+		<copyright>
+			<year>2004</year>
+			<year>2005</year>
+			<year>2006</year>
+			<year>2007</year>
+			<year>2008</year>
+			<holder>Amarendran R. Subramanian (DIALIGN-TX)</holder>
+		</copyright>
+    
+    <copyright>
+      <year>2004</year>
+      <holder>Volker Menrad (DIALIGN-TX)</holder>
+    </copyright>
+    
+    <copyright>
+      <year>2004</year>
+      <holder>Dorothea Emig (DIALIGN-TX)</holder>
+    </copyright>
+    
+		<copyright>
+			<year>2007</year>
+			<year>2008</year>
+			<holder>&dhusername; (This document and its XML source.)</holder>
+		</copyright>
+    
+		<legalnotice>
+     <para>
+       DIALIGN-TX is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version.
+     </para>
+     <para>
+       DIALIGN-TX is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.
+     </para>
+     <para>
+       You should have received a copy of the GNU Lesser General Public License along with this library; if not, write to the Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301  USA
+     </para>
+     <para>
+       On Debian system, a copy of the GNU Lesser General Public License is available in <filename class="directory">/usr/share/common-licences</filename>.
+     </para>
+     <para>
+       This documentation and its XML source file can be used, modified and redistributed under the same terms as DIALIGN-TX itself.
+     </para>
+    </legalnotice>
+	</refentryinfo>
+  
+	<refmeta>
+		<refentrytitle>&dhucpackage;</refentrytitle>
+		<manvolnum>&dhsection;</manvolnum>
+	</refmeta>
+	<refnamediv>
+		<refname>&dhpackage;</refname>
+		<refpurpose>Segment-based multiple sequence alignment</refpurpose>
+	</refnamediv>
+  
+	<refsynopsisdiv>
+		<cmdsynopsis>
+			<command>&dhpackage;</command>
+			<arg choice="opt"><option>OPTIONS</option></arg>
+      <arg choice="req"><replaceable>conf-directory</replaceable></arg>
+      <arg choice="req"><replaceable>fasta-file</replaceable></arg>
+			<arg choice="opt"><replaceable>fasta-out-file</replaceable></arg>
+		</cmdsynopsis>
+	</refsynopsisdiv>
+  
+	<refsect1 id="description">
+		<title>DESCRIPTION</title>
+		<para>
+      DIALIGN-TX is an improved algorithm for segment-based multiple protein alignments. DIALIGN-TX is a complete reimplementation of the segment-base approach including several new improvements and heuristics that significantly enhance the quality of the output alignments compared to DIALIGN 2.2. This significant superiority has been observed on local as well on global alignment benchmarks.
+    </para>
+	</refsect1>
+  
+	<refsect1 id="options">
+		<title>OPTIONS</title>
+		<variablelist>
+			<!-- Use the variablelist.term.separator and the
+			     variablelist.term.break.after parameters to
+			     control the term elements. -->
+      
+      <varlistentry>
+        <term><option>-d</option></term>
+        <listitem>
+          <para>Debug-Mode  [DEFAULT 0]</para>
+          <simplelist>
+            <member>0 no debug statements</member>
+            <member>1 debugs the current phase of the processing</member>
+            <member>2 very loquacious debugging</member>
+            <member>5 hardcore debugging</member>
+          </simplelist>
+        </listitem>
+      </varlistentry>
+      
+      <varlistentry>
+        <term><option>-s</option></term>
+        <listitem>
+          <para>Maximum amount of input sequences [DEFAULT 5000].</para>
+        </listitem>
+      </varlistentry>
+      
+      <varlistentry>
+        <term><option>-a</option></term>
+        <listitem>
+          <para>Maximum number of characters per line in a FASTA file [DEFAULT 100].</para>
+        </listitem>
+      </varlistentry>
+      
+      <varlistentry>
+        <term><option>-c</option></term>
+        <listitem>
+          <para>Maximum amount of characters per line when printing a sequence
+        [DEFAULT 80].</para>
+        </listitem>
+      </varlistentry>
+      
+      <varlistentry>
+	<term><option>-l</option></term>
+	<listitem>
+	<para>
+	  sensitivity mode, the higher the level the less likely spurious random fragments are aligned in local alignments [DEFAULT 0]
+	  <simplelist>
+	    <member>0 switched off</member>
+	    <member>1 level-1, reduced sensitivity</member>
+	    <member>2 level-2, strongly reduced sensitivity</member>
+	  </simplelist>
+	</para>
+	</listitem>
+      </varlistentry>
+      
+      <varlistentry>
+        <term><option>-m</option></term>
+        <listitem>
+          <para>
+            Score matrix file name (in the configuration directory) [DEFAULT PROTEIN: BLOSUM.scr] / [DEFAULT DNA: dna_matrix.scr].
+          </para>
+        </listitem>
+      </varlistentry>
+      
+      <varlistentry>
+        <term><option>-w</option></term>
+        <listitem>
+          <para>
+            Defines the minimum weight when the weight formula is changed to 1-pow(1-prob, factor) [DEFAULT 0.000000065].
+          </para>
+        </listitem>
+      </varlistentry>
+      
+      <varlistentry>
+        <term><option>-p</option></term>
+        <listitem>
+          <para>
+            Probability distribution file name (in the configuration directory) [DEFAULT PROTEIN: BLOSUM.diag_prob_t10] / [DEFAULT DNA: dna_diag_prob_100_exp_550000].
+          </para>
+        </listitem>
+      </varlistentry>
+      
+        
+      <varlistentry>
+        <term><option>-v</option></term>
+        <listitem>
+          <para>
+              Add to each score (to prevent negative values) [DEFAULT 0].
+          </para>
+        </listitem>
+      </varlistentry>
+        
+      <varlistentry>
+        <term><option>-t</option></term>
+        <listitem>
+          <para>
+            <quote>Even</quote> threshold for low score for sequences alignment [DEFAULT PROTEIN: 4] / [DEFAULT DNA: 0].
+          </para>
+        </listitem>
+      </varlistentry>
+        
+      <varlistentry>
+        <term><option>-n</option></term>
+        <listitem>
+          <para>
+            Maximum number of consecutive positions for window containing low scoring positions [DEFAULT PROTEIN: 4] / [DEFAULT DNA: 1].
+          </para>
+        </listitem>
+      </varlistentry>
+        
+      <varlistentry>
+        <term><option>-g</option></term>
+        <listitem>
+          <para>Global minimum fragment length for stop criterion [DEFAULT PROTEIN: 40] / [DEFAULT DNA: 1].
+          </para>
+        </listitem>
+      </varlistentry>
+        
+      <varlistentry>
+        <term><option>-m</option></term>
+        <listitem>
+          <para>
+            Minimal allowed average score in frag window containing low scoring positions [DEFAULT PROTEIN: 4.0] / [DEFAULT DNA: 0.9].
+          </para>
+        </listitem>
+      </varlistentry>
+        
+      <varlistentry>
+        <term><option>-o</option></term>
+        <listitem>
+          <para>Wether overlap weights are calculated or not [DEFAULT 0].</para>
+        </listitem>
+      </varlistentry>
+        
+      <varlistentry>
+        <term><option>-f</option></term>
+        <listitem>
+          <para>Minimum fragment length [DEFAULT 1].</para>
+        </listitem>
+      </varlistentry>
+        
+      <varlistentry>
+        <term><option>-r</option></term>
+        <listitem>
+          <para>Threshold weight to consider the fragment at all [DEFAULT 0.0]. </para>
+        </listitem>
+      </varlistentry>
+        
+      <varlistentry>
+        <term><option>-u</option></term>
+        <listitem>
+          <para>[DEFAULT 0]</para>
+          <simplelist>
+            <member>
+              1: Only use a sqrt(amount_of_seqs) stripe of neighbour sequences to calculate pairwise alignments (increase performance).
+            </member>
+            <member>
+              0: All pairwise alignments will be calculated.
+            </member>
+          </simplelist>
+        </listitem>
+      </varlistentry>
+        
+      <varlistentry>
+        <term><option>-A</option></term>
+        <listitem>
+          <para>Optional anchor file. [DEFAULT none]</para>
+        </listitem>
+      </varlistentry>
+        
+      <varlistentry>
+        <term><option>-D</option></term>
+        <listitem>
+          <para>Input is DNA-sequence.</para>
+        </listitem>
+      </varlistentry>
+        
+      <varlistentry>
+        <term><option>-T</option></term>
+        <listitem>
+          <para>
+            Translate DNA into aminoacids from begin to end (length will be cut to mod 3 = 0). <warning><para>Do not use <option>-D</option> with this option (Default values for PROTEIN input will be loaded).</para></warning>
+          </para>
+        </listitem>
+      </varlistentry>
+        
+      <varlistentry>
+        <term><option>-L</option></term>
+        <listitem>
+          <para>
+            Compare only longest Open Reading Frame. <warning><para>Do not use <option>-D</option> with this option (Default values for PROTEIN input will be loaded).</para></warning>
+          </para>
+        </listitem>
+      </varlistentry>
+        
+      <varlistentry>
+        <term><option>-O</option></term>
+        <listitem>
+          <para>
+            Translate DNA to aminoacids, reading frame for each sequence calculated due to its longest ORF. <warning><para>Do not use <option>-D</option> with this option (Default values for PROTEIN input will be loaded).</para></warning>
+          </para>
+        </listitem>
+      </varlistentry>
+        
+      <varlistentry>
+        <term><option>-P</option></term>
+        <listitem>
+          <para>
+            Output in aminoacids, no retranslation of DNA sequences [DEFAULT: input = output].
+          </para>
+        </listitem>
+      </varlistentry>
+      
+      <varlistentry>
+        <term><option>-F</option></term>
+	<listitem>
+	  <para>
+	    Fast mode (implies -l0, since it already significantly reduces sensitivity).
+	  </para>
+	</listitem>
+      </varlistentry>
+      
+      <varlistentry>
+        <term><option>-C</option></term>
+        <listitem>
+          <para>
+            Generate probability table saved in &config-dir;/prob_table and exit.
+          </para>
+        </listitem>
+      </varlistentry>
+        
+      <varlistentry>
+        <term><option>-H</option></term>
+        <term><option>-h</option></term>
+        <listitem>
+          <para> Print this message.
+          </para>
+        </listitem>
+      </varlistentry>
+		</variablelist>
+	</refsect1>
+  
+	<refsect1 id="files">
+		<title>FILES</title>
+		<variablelist>
+			<varlistentry>
+				<term><filename>&config-dir;</filename></term>
+				<listitem>
+					<para>
+            This is the default conf-directory that <command>&dhpackage;</command> expects as its first argument, as supplied in the upstream sources.
+          </para>
+				</listitem>
+			</varlistentry>
+		</variablelist>
+	</refsect1>
+
+	<refsect1 id="see_also">
+		<title>SEE ALSO</title>
+		<para>DIALIGN-TX is a re-implementation of <citerefentry><refentrytitle>dialign2-2</refentrytitle><manvolnum>1</manvolnum></citerefentry>. (See http://dialign.gobics.de/ for more information about DIALIGN2).
+		</para>
+		<para>The website of DIALIGN-TX is http://dialign-tx.gobics.de/</para>
+	</refsect1>
+
+	<refsect1 id="reference">
+		<title>REFERENCES</title>
+		<para>
+		  Amarendran R. Subramanian, Michael Kaufmann, Burkhard Morgenstern: DIALIGN-TX: improvement of the segment-based approach for multiple sequence alignment by combining greedy and progressive alignment strategies, Algorithms for Molecular Biology 3:6, 2008.
+		</para>
+		<para>
+		  Amarendran R. Subramanian, Jan Weyer-Menkhoff, Michael Kaufmann, Burkhard Morgenstern: DIALIGN-T: An improved algorithm for segment-based multiple sequence alignment. BMC Bioinformatics 2005, 6:66.
+		</para>
+	</refsect1>
+</refentry>
--- dialign-t-1.0.2.orig/debian/changelog
+++ dialign-t-1.0.2/debian/changelog
@@ -0,0 +1,51 @@
+dialign-t (1.0.2-1) unstable; urgency=low
+
+  * New upstream release:
+    - Fixes memory handling with anchor points.
+    - New option: -A optional anchor file [DEFAULT none]
+  * debian/dialign-tx.1*: documented the -A option.
+  * debian/co{mpat,trol}: using Debhelper 7.
+
+ -- Charles Plessy <plessy@debian.org>  Mon, 15 Dec 2008 14:12:59 +0900
+
+dialign-t (1.0.1-2) unstable; urgency=low
+
+  * debian/control:
+    - dialign-tx-data recommends dialign-tx, not dialign-t.
+    - Checked conformance with Policy 3.8.0 (no changes needed).
+
+ -- Charles Plessy <plessy@debian.org>  Sat, 21 Jun 2008 13:29:00 +0900
+
+dialign-t (1.0.1-1) unstable; urgency=low
+
+  * New upstream release updating bibliographic reference.
+  * debian/copyright: cosmetic changes.
+  * debian/dialign.1*:
+    - Converted DiAlign to DIALIGN;
+    - updated reference;
+    - incremented copyright year and version number.
+  * debian/control: updated reference.
+
+ -- Charles Plessy <plessy@debian.org>  Tue, 03 Jun 2008 19:58:50 +0900
+
+dialign-t (1.0.0-1) unstable; urgency=low
+
+  [ David Paleino ]
+  * Updated to Standards-Version 3.7.3 (no changes needed)
+
+  [ Charles Plessy ]
+  * New upstream version, renamed DIALIGN-TX.
+  * debian/control: Enhances: t-coffee.
+  * debian/copyright:
+    - Converted to machine-readable format.
+    - Updated relevant copyrights for 2008.
+  * Updated my email address.
+
+ -- Charles Plessy <plessy@debian.org>  Sat, 03 May 2008 11:16:37 +0900
+
+dialign-t (0.2.2.dfsg-1) unstable; urgency=low
+
+  * Removed upstream documentation.
+  * Initial release (Closes: #445983)
+
+ -- Charles Plessy <charles-debian-nospam@plessy.org>  Mon, 19 Nov 2007 23:45:20 +0900
--- dialign-t-1.0.2.orig/debian/dialign-tx.install
+++ dialign-t-1.0.2/debian/dialign-tx.install
@@ -0,0 +1 @@
+source/dialign-tx	usr/bin
--- dialign-t-1.0.2.orig/debian/compat
+++ dialign-t-1.0.2/debian/compat
@@ -0,0 +1 @@
+7
--- dialign-t-1.0.2.orig/debian/dialign-tx.1
+++ dialign-t-1.0.2/debian/dialign-tx.1
@@ -0,0 +1,266 @@
+.\"     Title: DIALIGN-TX
+.\"    Author: Amarendran R. Subramanian <subraman@informatik.uni-tuebingen.de>
+.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
+.\"      Date: 12/15/2008
+.\"    Manual: DIALIGN-TX: Parameters
+.\"    Source: dialign-tx 1.0.2
+.\"
+.TH "DIALIGN\-TX" "1" "12/15/2008" "dialign-tx 1.0.2" "DIALIGN-TX: Parameters"
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.SH "NAME"
+dialign-tx \- Segment-based multiple sequence alignment
+.SH "SYNOPSIS"
+.HP 11
+\fBdialign\-tx\fR [\fBOPTIONS\fR] {\fIconf\-directory\fR} {\fIfasta\-file\fR} [\fIfasta\-out\-file\fR]
+.SH "DESCRIPTION"
+.PP
+DIALIGN\-TX is an improved algorithm for segment\-based multiple protein alignments\&. DIALIGN\-TX is a complete reimplementation of the segment\-base approach including several new improvements and heuristics that significantly enhance the quality of the output alignments compared to DIALIGN 2\&.2\&. This significant superiority has been observed on local as well on global alignment benchmarks\&.
+.SH "OPTIONS"
+.PP
+\fB\-d\fR
+.RS 4
+Debug\-Mode [DEFAULT 0]
+.IP "" 4
+0 no debug statements
+.IP "" 4
+1 debugs the current phase of the processing
+.IP "" 4
+2 very loquacious debugging
+.IP "" 4
+5 hardcore debugging
+.RE
+.PP
+\fB\-s\fR
+.RS 4
+Maximum amount of input sequences [DEFAULT 5000]\&.
+.RE
+.PP
+\fB\-a\fR
+.RS 4
+Maximum number of characters per line in a FASTA file [DEFAULT 100]\&.
+.RE
+.PP
+\fB\-c\fR
+.RS 4
+Maximum amount of characters per line when printing a sequence [DEFAULT 80]\&.
+.RE
+.PP
+\fB\-l\fR
+.RS 4
+sensitivity mode, the higher the level the less likely spurious random fragments are aligned in local alignments [DEFAULT 0]
+.IP "" 4
+0 switched off
+.IP "" 4
+1 level\-1, reduced sensitivity
+.IP "" 4
+2 level\-2, strongly reduced sensitivity
+.RE
+.PP
+\fB\-m\fR
+.RS 4
+Score matrix file name (in the configuration directory) [DEFAULT PROTEIN: BLOSUM\&.scr] / [DEFAULT DNA: dna_matrix\&.scr]\&.
+.RE
+.PP
+\fB\-w\fR
+.RS 4
+Defines the minimum weight when the weight formula is changed to 1\-pow(1\-prob, factor) [DEFAULT 0\&.000000065]\&.
+.RE
+.PP
+\fB\-p\fR
+.RS 4
+Probability distribution file name (in the configuration directory) [DEFAULT PROTEIN: BLOSUM\&.diag_prob_t10] / [DEFAULT DNA: dna_diag_prob_100_exp_550000]\&.
+.RE
+.PP
+\fB\-v\fR
+.RS 4
+Add to each score (to prevent negative values) [DEFAULT 0]\&.
+.RE
+.PP
+\fB\-t\fR
+.RS 4
+
+\(lqEven\(rq
+threshold for low score for sequences alignment [DEFAULT PROTEIN: 4] / [DEFAULT DNA: 0]\&.
+.RE
+.PP
+\fB\-n\fR
+.RS 4
+Maximum number of consecutive positions for window containing low scoring positions [DEFAULT PROTEIN: 4] / [DEFAULT DNA: 1]\&.
+.RE
+.PP
+\fB\-g\fR
+.RS 4
+Global minimum fragment length for stop criterion [DEFAULT PROTEIN: 40] / [DEFAULT DNA: 1]\&.
+.RE
+.PP
+\fB\-m\fR
+.RS 4
+Minimal allowed average score in frag window containing low scoring positions [DEFAULT PROTEIN: 4\&.0] / [DEFAULT DNA: 0\&.9]\&.
+.RE
+.PP
+\fB\-o\fR
+.RS 4
+Wether overlap weights are calculated or not [DEFAULT 0]\&.
+.RE
+.PP
+\fB\-f\fR
+.RS 4
+Minimum fragment length [DEFAULT 1]\&.
+.RE
+.PP
+\fB\-r\fR
+.RS 4
+Threshold weight to consider the fragment at all [DEFAULT 0\&.0]\&.
+.RE
+.PP
+\fB\-u\fR
+.RS 4
+[DEFAULT 0]
+.IP "" 4
+
+              1: Only use a sqrt(amount_of_seqs) stripe of neighbour sequences to calculate pairwise alignments (increase performance)\&.
+            
+.IP "" 4
+
+              0: All pairwise alignments will be calculated\&.
+            
+.RE
+.PP
+\fB\-A\fR
+.RS 4
+Optional anchor file\&. [DEFAULT none]
+.RE
+.PP
+\fB\-D\fR
+.RS 4
+Input is DNA\-sequence\&.
+.RE
+.PP
+\fB\-T\fR
+.RS 4
+Translate DNA into aminoacids from begin to end (length will be cut to mod 3 = 0)\&.
+.sp
+.it 1 an-trap
+.nr an-no-space-flag 1
+.nr an-break-flag 1
+.br
+Warning
+Do not use
+\fB\-D\fR
+with this option (Default values for PROTEIN input will be loaded)\&.
+
+.RE
+.PP
+\fB\-L\fR
+.RS 4
+Compare only longest Open Reading Frame\&.
+.sp
+.it 1 an-trap
+.nr an-no-space-flag 1
+.nr an-break-flag 1
+.br
+Warning
+Do not use
+\fB\-D\fR
+with this option (Default values for PROTEIN input will be loaded)\&.
+
+.RE
+.PP
+\fB\-O\fR
+.RS 4
+Translate DNA to aminoacids, reading frame for each sequence calculated due to its longest ORF\&.
+.sp
+.it 1 an-trap
+.nr an-no-space-flag 1
+.nr an-break-flag 1
+.br
+Warning
+Do not use
+\fB\-D\fR
+with this option (Default values for PROTEIN input will be loaded)\&.
+
+.RE
+.PP
+\fB\-P\fR
+.RS 4
+Output in aminoacids, no retranslation of DNA sequences [DEFAULT: input = output]\&.
+.RE
+.PP
+\fB\-F\fR
+.RS 4
+Fast mode (implies \-l0, since it already significantly reduces sensitivity)\&.
+.RE
+.PP
+\fB\-C\fR
+.RS 4
+Generate probability table saved in /usr/share/dialign\-tx/prob_table and exit\&.
+.RE
+.PP
+\fB\-H\fR, \fB\-h\fR
+.RS 4
+Print this message\&.
+.RE
+.SH "FILES"
+.PP
+\fI/usr/share/dialign\-tx\fR
+.RS 4
+This is the default conf\-directory that
+\fBdialign\-tx\fR
+expects as its first argument, as supplied in the upstream sources\&.
+.RE
+.SH "SEE ALSO"
+.PP
+DIALIGN\-TX is a re\-implementation of
+\fBdialign2-2\fR(1)\&. (See http://dialign\&.gobics\&.de/ for more information about DIALIGN2)\&.
+.PP
+The website of DIALIGN\-TX is http://dialign\-tx\&.gobics\&.de/
+.SH "REFERENCES"
+.PP
+Amarendran R\&. Subramanian, Michael Kaufmann, Burkhard Morgenstern: DIALIGN\-TX: improvement of the segment\-based approach for multiple sequence alignment by combining greedy and progressive alignment strategies, Algorithms for Molecular Biology 3:6, 2008\&.
+.PP
+Amarendran R\&. Subramanian, Jan Weyer\-Menkhoff, Michael Kaufmann, Burkhard Morgenstern: DIALIGN\-T: An improved algorithm for segment\-based multiple sequence alignment\&. BMC Bioinformatics 2005, 6:66\&.
+.SH "AUTHORS"
+.PP
+\fBAmarendran R\&. Subramanian\fR <\&subraman@informatik\&.uni\-tuebingen\&.de\&>
+.sp -1n
+.IP "" 4
+Author of dialign\-tx
+.PP
+\fBVolker Menrad\fR
+.sp -1n
+.IP "" 4
+Co\-author of dialign\-tx
+.PP
+\fBDorothea Emig\fR
+.sp -1n
+.IP "" 4
+Co\-author of dialign\-tx
+.PP
+\fBCharles Plessy\fR <\&plessy@debian\&.org\&>
+.sp -1n
+.IP "" 4
+Converted this guide in DocBook XML for the Debian distribution\&.
+.SH "COPYRIGHT"
+Copyright \(co 2004, 2005, 2006, 2007, 2008 Amarendran R. Subramanian (DIALIGN-TX)
+.br
+Copyright \(co 2004 Volker Menrad (DIALIGN-TX)
+.br
+Copyright \(co 2004 Dorothea Emig (DIALIGN-TX)
+.br
+Copyright \(co 2007, 2008 Charles Plessy (This document and its XML source.)
+.br
+.PP
+DIALIGN\-TX is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2\&.1 of the License, or (at your option) any later version\&.
+.PP
+DIALIGN\-TX is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE\&. See the GNU Lesser General Public License for more details\&.
+.PP
+You should have received a copy of the GNU Lesser General Public License along with this library; if not, write to the Free Software Foundation, Inc\&., 51 Franklin St, Fifth Floor, Boston, MA 02110\-1301 USA
+.PP
+On Debian system, a copy of the GNU Lesser General Public License is available in
+\fI/usr/share/common\-licences\fR\&.
+.PP
+This documentation and its XML source file can be used, modified and redistributed under the same terms as DIALIGN\-TX itself\&.
+.sp
--- dialign-t-1.0.2.orig/debian/copyright
+++ dialign-t-1.0.2/debian/copyright
@@ -0,0 +1,32 @@
+Format-Specification: http://wiki.debian.org/Proposals/CopyrightFormat?action=recall&rev=129
+Upstream-Author: Amarendran R. Subramanian <subraman@informatik.uni-tuebingen.de>
+X-Packaged-By: Charles Plessy <plessy@debian.org>
+X-Packaged-Date: Tue,  9 Oct 2007 23:17:04 +0900
+Original-Source-Location: http://dialign-tx.gobics.de/DIALIGN-TX_1.0.2.tar.gz
+
+Files: *
+Copyright: © 2004-2008 Amarendran R. Subramanian
+           © 2004      Volker Menrad
+           © 2004      Dorothea Emig 
+License: LGPL-2.1+
+ This package is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 2.1 of the License, or (at your option) any later version.
+ .
+ This package is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+ Lesser General Public License for more details.
+ .
+ You should have received a copy of the GNU Lesser General Public
+ License along with this package; if not, write to the Free Software
+ Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301 USA
+X-Comment: On Debian systems, the complete text of the GNU Lesser General
+ Public License can be found in `/usr/share/common-licenses/LGPL'.
+
+Files: debian/*
+Copyright: © 2007-2008 Charles Plessy <plessy@debian.org>
+           © 2008      David Paleino <d.paleino@gmail.com>
+License: LGPL-2.1+
+ The Debian packaging is licensed under the same terms as DIALIGN-TX itself.