[med-svn] r1674 - trunk/packages/dialign-t/trunk/debian
charles-guest at alioth.debian.org
charles-guest at alioth.debian.org
Mon Mar 31 12:01:59 UTC 2008
Author: charles-guest
Date: 2008-03-31 12:01:58 +0000 (Mon, 31 Mar 2008)
New Revision: 1674
Added:
trunk/packages/dialign-t/trunk/debian/dialign-tx-data.install
trunk/packages/dialign-t/trunk/debian/dialign-tx.1
trunk/packages/dialign-t/trunk/debian/dialign-tx.1.xml
trunk/packages/dialign-t/trunk/debian/dialign-tx.install
Removed:
trunk/packages/dialign-t/trunk/debian/dialign-t-data.install
trunk/packages/dialign-t/trunk/debian/dialign-t-doc.doc-base
trunk/packages/dialign-t/trunk/debian/dialign-t.1
trunk/packages/dialign-t/trunk/debian/dialign-t.1.xml
trunk/packages/dialign-t/trunk/debian/dialign-t.install
Modified:
trunk/packages/dialign-t/trunk/debian/changelog
trunk/packages/dialign-t/trunk/debian/control
trunk/packages/dialign-t/trunk/debian/copyright
trunk/packages/dialign-t/trunk/debian/rules
trunk/packages/dialign-t/trunk/debian/watch
Log:
DIALIGN -T renamed DIALIGN-TX upstream; work in progress to reflect this in the package.
Modified: trunk/packages/dialign-t/trunk/debian/changelog
===================================================================
--- trunk/packages/dialign-t/trunk/debian/changelog 2008-03-31 11:25:14 UTC (rev 1673)
+++ trunk/packages/dialign-t/trunk/debian/changelog 2008-03-31 12:01:58 UTC (rev 1674)
@@ -1,14 +1,14 @@
-dialign-t (1:0.2.2-1) UNRELEASED; urgency=low
+dialign-t (1.0.0-1) UNRELEASED; 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.
- * Since the sources of the documentation are lost, it is not
- necessary to remove it, as it does not violate the DFSG.
- * debian/changelog: added an epoch.
- * Changed the doc-base section according to the new policy.
+ * debian/copyright:
+ - Converted to machine-readable format.
+ - Updated relevant copyrights for 2008.
-- Charles Plessy <charles-debian-nospam at plessy.org> Sat, 22 Mar 2008 11:46:01 +0900
Modified: trunk/packages/dialign-t/trunk/debian/control
===================================================================
--- trunk/packages/dialign-t/trunk/debian/control 2008-03-31 11:25:14 UTC (rev 1673)
+++ trunk/packages/dialign-t/trunk/debian/control 2008-03-31 12:01:58 UTC (rev 1674)
@@ -8,30 +8,39 @@
Standards-Version: 3.7.3
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-t.gobics.de/
+Homepage: http://dialign-tx.gobics.de/
-Package: dialign-t
+Package: dialign-tx
Architecture: any
Depends: ${shlibs:Depends}, ${misc:Depends}, dialign-t-data (= ${source:Version})
Enhances: t-coffee
Description: Segment-based multiple sequence alignment
- DIALIGN-T is a command line tool to perform multiple alignment of protein or
+ 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. For pairwise
- alignment, DIALIGN-T uses a fragment-chaining algorithm that favours chains of
+ alignment, DIALIGN-TX
+CHECK
+ uses a fragment-chaining algorithm that favours chains of
low-scoring local alignments over isolated high-scoring fragments. For
multiple alignment, DIALIGN-T 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.
+ Submission in Progress, 2008.
+ .
DIALIGN-T has been published in 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.
+UPDATE
+
-Package: dialign-t-data
+Package: dialign-tx-data
Architecture: all
Depends: ${misc:Depends}
Recommends: dialign-t (= ${source:Version})
Description: Common data files for dialign-t
This package contain the score matrices and probability distribution files
- that DIALIGN-T needs to align peptidic and nucleic sequences.
+ that DIALIGN-TX needs to align peptidic and nucleic sequences.
Modified: trunk/packages/dialign-t/trunk/debian/copyright
===================================================================
--- trunk/packages/dialign-t/trunk/debian/copyright 2008-03-31 11:25:14 UTC (rev 1673)
+++ trunk/packages/dialign-t/trunk/debian/copyright 2008-03-31 12:01:58 UTC (rev 1674)
@@ -1,41 +1,39 @@
-This package was debianized by Charles Plessy <charles-debian-nospam at plessy.org> on
-Tue, 9 Oct 2007 23:17:04 +0900.
+X-Format-Specification: http://wiki.debian.org/Proposals/CopyrightFormat
+X-Debianized-By: Charles Plessy <charles-debian-nospam at plessy.org>
+X-Debianized-Date: Tue, 9 Oct 2007 23:17:04 +0900
+X-Source-Downloaded-From: http://dialign-tx.gobics.de
+X-Upstream-Author: Amarendran R. Subramanian <subraman at informatik.uni-tuebingen.de>
-It was downloaded from <http://dialign-t.gobics.de/> The documentation was then
-deleted with the following command: `rm -rf doc'. Then, the sources were
-repackaged under the name dialign-t_0.2.2.dfsg.orig.tar.gz
+Files: debian/*
-Upstream Authors:
+Copyright: © 2007-2008 Charles Plessy <charles-debian-nospam at plessy.org>
+ © 2008 David Paleino <d.paleino at gmail.com>
- Amarendran R. Subramanian <subraman at informatik.uni-tuebingen.de>
- Volker Menrad
- Dorothea Emig
+License: LGPL-2.1+
+ The Debian packaging is licensed under the same terms as DIALIGN-TX itself.
-Copyright:
- Copyright 2004-2007 Amarendran R. Subramanian
- Copyright 2004 Volker Menrad
- Copyright 2004 Dorothea Emig
+Files: *
-License:
+Copyright: © 2004-2007 Amarendran R. Subramanian
+ © 2004 Volker Menrad
+ © 2004 Dorothea Emig
- 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.
+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
- 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
-
-On Debian systems, the complete text of the GNU Lesser General
-Public License can be found in `/usr/share/common-licenses/LGPL'.
-
-The Debian packaging is © 2007, Charles Plessy and is licensed under the same
-terms as DIALIGN-T itself.
+X-Comment: On Debian systems, the complete text of the GNU Lesser General
+ Public License can be found in `/usr/share/common-licenses/LGPL'.
Deleted: trunk/packages/dialign-t/trunk/debian/dialign-t-data.install
===================================================================
--- trunk/packages/dialign-t/trunk/debian/dialign-t-data.install 2008-03-31 11:25:14 UTC (rev 1673)
+++ trunk/packages/dialign-t/trunk/debian/dialign-t-data.install 2008-03-31 12:01:58 UTC (rev 1674)
@@ -1 +0,0 @@
-conf/* usr/share/dialign-t/
Deleted: trunk/packages/dialign-t/trunk/debian/dialign-t-doc.doc-base
===================================================================
--- trunk/packages/dialign-t/trunk/debian/dialign-t-doc.doc-base 2008-03-31 11:25:14 UTC (rev 1673)
+++ trunk/packages/dialign-t/trunk/debian/dialign-t-doc.doc-base 2008-03-31 12:01:58 UTC (rev 1674)
@@ -1,14 +0,0 @@
-Document: dialign-t-doc
-Title: DiAlign-T: Parameters
-Author: Volker Menrad
-Section: Science/Biology
-
-Format: PDF
-Files: /usr/share/doc/dialign-t-doc/user_guide.pdf
-
-Format: postscript
-Files: /usr/share/doc/dialign-t-doc/user_guide.ps
-
-Format: HTML
-Index: /usr/share/doc/dialign-t-doc/html/index.html
-Files: /usr/share/doc/dialign-t-doc/html/*.html
Deleted: trunk/packages/dialign-t/trunk/debian/dialign-t.1
===================================================================
--- trunk/packages/dialign-t/trunk/debian/dialign-t.1 2008-03-31 11:25:14 UTC (rev 1673)
+++ trunk/packages/dialign-t/trunk/debian/dialign-t.1 2008-03-31 12:01:58 UTC (rev 1674)
@@ -1,243 +0,0 @@
-.\" Title: DIALIGN-T
-.\" Author: Amarendran R. Subramanian <subraman at informatik.uni-tuebingen.de>
-.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 11/14/2007
-.\" Manual: DiAlign-T: Parameters
-.\" Source: dialign-t 0.2.2
-.\"
-.TH "DIALIGN\-T" "1" "11/14/2007" "dialign-t 0.2.2" "DiAlign-T: Parameters"
-.\" disable hyphenation
-.nh
-.\" disable justification (adjust text to left margin only)
-.ad l
-.SH "NAME"
-dialign-t - Segment-based multiple sequence alignment
-.SH "SYNOPSIS"
-.HP 10
-\fBdialign\-t\fR [\fBOPTIONS\fR] {\fIconf\-directory\fR} {\fIfasta\-file\fR} [\fIfasta\-out\-file\fR]
-.SH "DESCRIPTION"
-.PP
-DIALIGN\-T is an improved algorithm for segment\-based multiple protein alignments\. DIALIGN\-T 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\-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\-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\-C\fR
-.RS 4
-Generate probability table saved in /usr/share/dialign\-t/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\-t\fR
-.RS 4
-This is the default conf\-directory that
-\fBdialign\-t\fR
-expects as its first argument, as supplied in the upstream sources\.
-.RE
-.SH "SEE ALSO"
-.PP
-DIALIGN\-T is a re\-implementation of
-\fBdialign2-2\fR(1)\. (See http://dialign\.gobics\.de/ for more information about DIALIGN2)\.
-.PP
-The website of DIALIGN\-T is http://dialign\-t\.gobics\.de/
-.SH "REFERENCE"
-.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 at informatik\.uni\-tuebingen\.de\&>
-.sp -1n
-.IP "" 4
-Author of dialign\-t
-.PP
-\fBVolker Menrad\fR
-.sp -1n
-.IP "" 4
-Co\-author of dialign\-t
-.PP
-\fBDorothea Emig\fR
-.sp -1n
-.IP "" 4
-Co\-author of dialign\-t
-.PP
-\fBCharles Plessy\fR <\&charles\-debian\-nospam at plessy\.org\&>
-.sp -1n
-.IP "" 4
-Converted this guide in DocBook XML for the Debian distribution\.
-.SH "COPYRIGHT"
-Copyright \(co 2004, 2005, 2006, 2007 Amarendran R. Subramanian
-.br
-Copyright \(co 2004 Volker Menrad
-.br
-Copyright \(co 2004 Dorothea Emig
-.br
-Copyright \(co 2007 Charles Plessy
-.br
-.PP
-DiAlign\-T 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\-T 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\-T itself\.
-.sp
Deleted: trunk/packages/dialign-t/trunk/debian/dialign-t.1.xml
===================================================================
--- trunk/packages/dialign-t/trunk/debian/dialign-t.1.xml 2008-03-31 11:25:14 UTC (rev 1673)
+++ trunk/packages/dialign-t/trunk/debian/dialign-t.1.xml 2008-03-31 12:01:58 UTC (rev 1674)
@@ -1,378 +0,0 @@
-<?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 V4.4//EN"
- "http://www.oasis-open.org/docbook/xml/4.4/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 "charles-debian-nospam at plessy.org">
- <!ENTITY dhusername "&dhfirstname; &dhsurname;">
- <!ENTITY dhrelease "0.2.2">
- <!ENTITY dhtitle "DiAlign-T: Parameters">
- <!ENTITY dhucpackage "DIALIGN-T">
- <!ENTITY dhpackage "dialign-t">
- <!ENTITY dhproduct "&dhpackage;">
- <!ENTITY dhsection "1">
-
- <!ENTITY config-dir "/usr/share/dialign-t">
-]>
-
-<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 at 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>
- <holder> Amarendran R. Subramanian</holder>
- </copyright>
-
- <copyright>
- <year>2004</year>
- <holder>Volker Menrad</holder>
- </copyright>
-
- <copyright>
- <year>2004</year>
- <holder>Dorothea Emig</holder>
- </copyright>
-
- <copyright>
- <year>2007</year>
- <holder>&dhusername;</holder>
- </copyright>
-
- <legalnotice>
- <para>
- DiAlign-T 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-T 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-T 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-T is an improved algorithm for segment-based multiple protein alignments. DIALIGN-T 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>-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>-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>-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-T 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-T is http://dialign-t.gobics.de/</para>
- </refsect1>
-
- <refsect1 id="reference">
- <title>REFERENCE</title>
- <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>
Deleted: trunk/packages/dialign-t/trunk/debian/dialign-t.install
===================================================================
--- trunk/packages/dialign-t/trunk/debian/dialign-t.install 2008-03-31 11:25:14 UTC (rev 1673)
+++ trunk/packages/dialign-t/trunk/debian/dialign-t.install 2008-03-31 12:01:58 UTC (rev 1674)
@@ -1 +0,0 @@
-source/dialign-t usr/bin
Copied: trunk/packages/dialign-t/trunk/debian/dialign-tx-data.install (from rev 1545, trunk/packages/dialign-t/trunk/debian/dialign-t-data.install)
===================================================================
--- trunk/packages/dialign-t/trunk/debian/dialign-tx-data.install (rev 0)
+++ trunk/packages/dialign-t/trunk/debian/dialign-tx-data.install 2008-03-31 12:01:58 UTC (rev 1674)
@@ -0,0 +1,2 @@
+conf/* usr/share/dialign-tx/
+data/* usr/share/dialign-tx/
Copied: trunk/packages/dialign-t/trunk/debian/dialign-tx.1 (from rev 1669, trunk/packages/dialign-t/trunk/debian/dialign-t.1)
===================================================================
--- trunk/packages/dialign-t/trunk/debian/dialign-tx.1 (rev 0)
+++ trunk/packages/dialign-t/trunk/debian/dialign-tx.1 2008-03-31 12:01:58 UTC (rev 1674)
@@ -0,0 +1,243 @@
+.\" Title: DIALIGN-T
+.\" Author: Amarendran R. Subramanian <subraman at informatik.uni-tuebingen.de>
+.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
+.\" Date: 11/14/2007
+.\" Manual: DiAlign-T: Parameters
+.\" Source: dialign-t 0.2.2
+.\"
+.TH "DIALIGN\-T" "1" "11/14/2007" "dialign-t 0.2.2" "DiAlign-T: Parameters"
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.SH "NAME"
+dialign-t - Segment-based multiple sequence alignment
+.SH "SYNOPSIS"
+.HP 10
+\fBdialign\-t\fR [\fBOPTIONS\fR] {\fIconf\-directory\fR} {\fIfasta\-file\fR} [\fIfasta\-out\-file\fR]
+.SH "DESCRIPTION"
+.PP
+DIALIGN\-T is an improved algorithm for segment\-based multiple protein alignments\. DIALIGN\-T 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\-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\-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\-C\fR
+.RS 4
+Generate probability table saved in /usr/share/dialign\-t/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\-t\fR
+.RS 4
+This is the default conf\-directory that
+\fBdialign\-t\fR
+expects as its first argument, as supplied in the upstream sources\.
+.RE
+.SH "SEE ALSO"
+.PP
+DIALIGN\-T is a re\-implementation of
+\fBdialign2-2\fR(1)\. (See http://dialign\.gobics\.de/ for more information about DIALIGN2)\.
+.PP
+The website of DIALIGN\-T is http://dialign\-t\.gobics\.de/
+.SH "REFERENCE"
+.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 at informatik\.uni\-tuebingen\.de\&>
+.sp -1n
+.IP "" 4
+Author of dialign\-t
+.PP
+\fBVolker Menrad\fR
+.sp -1n
+.IP "" 4
+Co\-author of dialign\-t
+.PP
+\fBDorothea Emig\fR
+.sp -1n
+.IP "" 4
+Co\-author of dialign\-t
+.PP
+\fBCharles Plessy\fR <\&charles\-debian\-nospam at plessy\.org\&>
+.sp -1n
+.IP "" 4
+Converted this guide in DocBook XML for the Debian distribution\.
+.SH "COPYRIGHT"
+Copyright \(co 2004, 2005, 2006, 2007 Amarendran R. Subramanian
+.br
+Copyright \(co 2004 Volker Menrad
+.br
+Copyright \(co 2004 Dorothea Emig
+.br
+Copyright \(co 2007 Charles Plessy
+.br
+.PP
+DiAlign\-T 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\-T 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\-T itself\.
+.sp
Copied: trunk/packages/dialign-t/trunk/debian/dialign-tx.1.xml (from rev 1669, trunk/packages/dialign-t/trunk/debian/dialign-t.1.xml)
===================================================================
--- trunk/packages/dialign-t/trunk/debian/dialign-tx.1.xml (rev 0)
+++ trunk/packages/dialign-t/trunk/debian/dialign-tx.1.xml 2008-03-31 12:01:58 UTC (rev 1674)
@@ -0,0 +1,378 @@
+<?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 V4.4//EN"
+ "http://www.oasis-open.org/docbook/xml/4.4/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 "charles-debian-nospam at plessy.org">
+ <!ENTITY dhusername "&dhfirstname; &dhsurname;">
+ <!ENTITY dhrelease "1.0.0">
+ <!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-t">
+]>
+
+<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 at 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>
+ <holder> Amarendran R. Subramanian</holder>
+ </copyright>
+
+ <copyright>
+ <year>2004</year>
+ <holder>Volker Menrad</holder>
+ </copyright>
+
+ <copyright>
+ <year>2004</year>
+ <holder>Dorothea Emig</holder>
+ </copyright>
+
+ <copyright>
+ <year>2007</year>
+ <holder>&dhusername;</holder>
+ </copyright>
+
+ <legalnotice>
+ <para>
+ DiAlign-T 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-T 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-T 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-T is an improved algorithm for segment-based multiple protein alignments. DIALIGN-T 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>-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>-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>-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-T 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-T is http://dialign-t.gobics.de/</para>
+ </refsect1>
+
+ <refsect1 id="reference">
+ <title>REFERENCE</title>
+ <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>
Copied: trunk/packages/dialign-t/trunk/debian/dialign-tx.install (from rev 1545, trunk/packages/dialign-t/trunk/debian/dialign-t.install)
===================================================================
--- trunk/packages/dialign-t/trunk/debian/dialign-tx.install (rev 0)
+++ trunk/packages/dialign-t/trunk/debian/dialign-tx.install 2008-03-31 12:01:58 UTC (rev 1674)
@@ -0,0 +1 @@
+source/dialign-tx usr/bin
Modified: trunk/packages/dialign-t/trunk/debian/rules
===================================================================
--- trunk/packages/dialign-t/trunk/debian/rules 2008-03-31 11:25:14 UTC (rev 1673)
+++ trunk/packages/dialign-t/trunk/debian/rules 2008-03-31 12:01:58 UTC (rev 1674)
@@ -6,8 +6,7 @@
ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS)))
CFLAGS += -O0
else
- CFLAGS += -Os
-# CFLAGS += -O2 Please revert to O2 when bug 446714 is fixed
+ CFLAGS += -O2 Please revert to O2 when bug 446714 is fixed
endif
build: build-stamp
@@ -29,7 +28,7 @@
dh_clean -k
dh_installdirs
dh_install
- chmod 644 $(CURDIR)/debian/dialign-t-data/usr/share/dialign-t/*
+ chmod 644 $(CURDIR)/debian/dialign-tx-data/usr/share/dialign-tx/*
binary-indep: build install
Modified: trunk/packages/dialign-t/trunk/debian/watch
===================================================================
--- trunk/packages/dialign-t/trunk/debian/watch 2008-03-31 11:25:14 UTC (rev 1673)
+++ trunk/packages/dialign-t/trunk/debian/watch 2008-03-31 12:01:58 UTC (rev 1674)
@@ -1,3 +1,4 @@
version=3
-opts="dversionmangle=s/.dfsg.*//" \
-http://dialign-t.gobics.de/ DIALIGN-T_(.*)\.tar\.gz
+#opts="dversionmangle=s/.dfsg.*//" \
+#opts="downloadurlmangle=s/download//" \
+http://dialign-tx.gobics.de/download DIALIGN-TX_(.*).tar.gz
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