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       dialign-tx - Segment-based multiple sequence alignment


       dialign-tx [OPTIONS] {conf-directory} {fasta-file} [fasta-out-file]


       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.


           Debug-Mode [DEFAULT 0]

               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].

           Maximum number of characters per line in a FASTA file [DEFAULT

           Maximum amount of characters per line when printing a sequence
           [DEFAULT 80].

           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

           Score matrix file name (in the configuration directory) [DEFAULT
           PROTEIN: BLOSUM.scr] / [DEFAULT DNA: dna_matrix.scr].

           Defines the minimum weight when the weight formula is changed to
           1-pow(1-prob, factor) [DEFAULT 0.000000065].

           Probability distribution file name (in the configuration directory)
           [DEFAULT PROTEIN: BLOSUM.diag_prob_t10] / [DEFAULT DNA:

           Add to each score (to prevent negative values) [DEFAULT 0].


           “Even” threshold for low score for sequences alignment [DEFAULT
           PROTEIN: 4] / [DEFAULT DNA: 0].

           Maximum number of consecutive positions for window containing low
           scoring positions [DEFAULT PROTEIN: 4] / [DEFAULT DNA: 1].

           Global minimum fragment length for stop criterion [DEFAULT PROTEIN:
           40] / [DEFAULT DNA: 1].

           Minimal allowed average score in frag window containing low scoring
           positions [DEFAULT PROTEIN: 4.0] / [DEFAULT DNA: 0.9].

           Wether overlap weights are calculated or not [DEFAULT 0].

           Minimum fragment length [DEFAULT 1].

           Threshold weight to consider the fragment at all [DEFAULT 0.0].

           [DEFAULT 0]

                             1: Only use a sqrt(amount_of_seqs) stripe of
               neighbour sequences to calculate pairwise alignments (increase

                             0: All pairwise alignments will be calculated.

           Optional anchor file. [DEFAULT none]

           Input is DNA-sequence.

           Translate DNA into aminoacids from begin to end (length will be cut
           to mod 3 = 0).

           Do not use -D with this option (Default values for PROTEIN input
           will be loaded).

           Compare only longest Open Reading Frame.

           Do not use -D with this option (Default values for PROTEIN input
           will be loaded).

           Translate DNA to aminoacids, reading frame for each sequence
           calculated due to its longest ORF.

           Do not use -D with this option (Default values for PROTEIN input
           will be loaded).

           Output in aminoacids, no retranslation of DNA sequences [DEFAULT:
           input = output].

           Fast mode (implies -l0, since it already significantly reduces

           Generate probability table saved in
           /usr/share/dialign-tx/prob_table and exit.

       -H, -h
           Print this message.


           This is the default conf-directory that dialign-tx expects as its
           first argument, as supplied in the upstream sources.


       DIALIGN-TX is a re-implementation of dialign2-2(1). (See for more information about DIALIGN2).

       The website of DIALIGN-TX is


       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,


       Amarendran R. Subramanian <>
           Author of dialign-tx

       Volker Menrad
           Co-author of dialign-tx

       Dorothea Emig
           Co-author of dialign-tx

       Charles Plessy <>
           Converted this guide in DocBook XML for the Debian distribution.


       Copyright © 2004, 2005, 2006, 2007, 2008 Amarendran R. Subramanian
       Copyright © 2004 Volker Menrad (DIALIGN-TX)
       Copyright © 2004 Dorothea Emig (DIALIGN-TX)
       Copyright © 2007, 2008 Charles Plessy (This document and its XML

       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
       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

       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.