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dialign-tx - Online in the Cloud

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This is the command dialign-tx that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

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
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.

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