.\" Title: DIALIGN-TX .\" Author: Amarendran R. Subramanian .\" Generator: DocBook XSL Stylesheets v1.73.2 .\" 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 Whether 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