SYNOPSIS
- dialign-tx [OPTIONS] {conf-directory} {fasta-file} [fasta-out-file]
DESCRIPTION
OPTIONS
-d
-
Debug-Mode [DEFAULT 0]
- 0 no debug statements
- 1 debugs the current phase of the processing
- 2 very loquacious debugging
- 5 hardcore debugging
-s
- Maximum amount of input sequences [DEFAULT 5000].
-a
- Maximum number of characters per line in a FASTA file [DEFAULT 100].
-c
- Maximum amount of characters per line when printing a sequence [DEFAULT 80].
-l
-
sensitivity mode, the higher the level the less likely spurious random fragments are aligned in local alignments [DEFAULT 0]
- 0 switched off
- 1 level-1, reduced sensitivity
- 2 level-2, strongly reduced sensitivity
-m
- Score matrix file name (in the configuration directory) [DEFAULT PROTEIN: BLOSUM.scr] / [DEFAULT DNA: dna_matrix.scr].
-w
- Defines the minimum weight when the weight formula is changed to 1-pow(1-prob, factor) [DEFAULT 0.000000065].
-p
- Probability distribution file name (in the configuration directory) [DEFAULT PROTEIN: BLOSUM.diag_prob_t10] / [DEFAULT DNA: dna_diag_prob_100_exp_550000].
-v
- Add to each score (to prevent negative values) [DEFAULT 0].
-t
-
"Even" threshold for low score for sequences alignment [DEFAULT PROTEIN: 4] / [DEFAULT DNA: 0].
-n
- Maximum number of consecutive positions for window containing low scoring positions [DEFAULT PROTEIN: 4] / [DEFAULT DNA: 1].
-g
- Global minimum fragment length for stop criterion [DEFAULT PROTEIN: 40] / [DEFAULT DNA: 1].
-m
- Minimal allowed average score in frag window containing low scoring positions [DEFAULT PROTEIN: 4.0] / [DEFAULT DNA: 0.9].
-o
- Whether overlap weights are calculated or not [DEFAULT 0].
-f
- Minimum fragment length [DEFAULT 1].
-r
- Threshold weight to consider the fragment at all [DEFAULT 0.0].
-u
-
[DEFAULT 0]
-
1: Only use a sqrt(amount_of_seqs) stripe of neighbour sequences to calculate pairwise alignments (increase performance).
-
0: All pairwise alignments will be calculated.
-
-A
- Optional anchor file. [DEFAULT none]
-D
- Input is DNA-sequence.
-T
-
Translate DNA into aminoacids from begin to end (length will be cut to mod 3 = 0).
Warning Do not use -D with this option (Default values for PROTEIN input will be loaded).
-L
-
Compare only longest Open Reading Frame.
Warning Do not use -D with this option (Default values for PROTEIN input will be loaded).
-O
-
Translate DNA to aminoacids, reading frame for each sequence calculated due to its longest ORF.
Warning Do not use -D with this option (Default values for PROTEIN input will be loaded).
-P
- Output in aminoacids, no retranslation of DNA sequences [DEFAULT: input = output].
-F
- Fast mode (implies -l0, since it already significantly reduces sensitivity).
-C
- Generate probability table saved in /usr/share/dialign-tx/prob_table and exit.
-H, -h
- Print this message.
FILES
/usr/share/dialign-tx
- This is the default conf-directory that dialign-tx expects as its first argument, as supplied in the upstream sources.
REFERENCES
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.
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.
AUTHORS
Amarendran R. Subramanian <[email protected]>
- Author of dialign-tx
Volker Menrad
- Co-author of dialign-tx
Dorothea Emig
- Co-author of dialign-tx
Charles Plessy <[email protected]>
- Converted this guide in DocBook XML for the Debian distribution.
COPYRIGHT
Copyright © 2004, 2005, 2006, 2007, 2008 Amarendran R. Subramanian (DIALIGN-TX)Copyright © 2004 Volker Menrad (DIALIGN-TX)
Copyright © 2004 Dorothea Emig (DIALIGN-TX)
Copyright © 2007, 2008 Charles Plessy (This document and its XML source.)
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.
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.
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
On Debian system, a copy of the GNU Lesser General Public License is available in /usr/share/common-licences.
This documentation and its XML source file can be used, modified and redistributed under the same terms as DIALIGN-TX itself.