table of contents
DIALIGN-TX(1) | DIALIGN-TX: Parameters | DIALIGN-TX(1) |
NAME¶
dialign-tx - Segment-based multiple sequence alignmentSYNOPSIS¶
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¶
-dDebug-Mode [DEFAULT 0]
-s
- 0 no debug statements
- 1 debugs the current phase of the processing
- 2 very loquacious debugging
- 5 hardcore debugging
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]
-m
- 0 switched off
- 1 level-1, reduced sensitivity
- 2 level-2, strongly reduced sensitivity
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]
-A
-
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.
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-txThis 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
- Co-author of dialign-tx
- Co-author of dialign-tx
- Converted this guide in DocBook XML for the Debian distribution.
COPYRIGHT¶
Copyright © 2004, 2005, 2006, 2007, 2008 Amarendran R. Subramanian (DIALIGN-TX)12/15/2008 | dialign-tx 1.0.2 |