NAME
dialign-tx - Segment-based multiple sequence alignment
SYNOPSIS
dialign-tx [OPTIONS] {conf-directory} {fasta-file} [fasta-out-file]
DESCRIPTION
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.
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
Wether 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.
SEE ALSO
DIALIGN-TX is a re-implementation of dialign2-2(1). (See
http://dialign.gobics.de/ for more information about DIALIGN2).
The website of DIALIGN-TX is http://dialign-tx.gobics.de/
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 <subraman@informatik.uni-tuebingen.de>
Author of dialign-tx
Volker Menrad
Co-author of dialign-tx
Dorothea Emig
Co-author of dialign-tx
Charles Plessy <plessy@debian.org>
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.