DIALIGN-TX(1)

📦 version 1.0.2, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu resolute, ubuntu stonking

✨ DIALIGN-TX(1) — the vibe ✨

okay bestie, gather round, because this is the manual page for dialign-tx, aka section 1 of your local Unix manuals, and it's literally about smashing multiple protein sequences together into one beautiful alignment. it's giving science. it's giving 💅. let's go.

🌸 NAME 🌸

dialign-tx — segment-based multiple sequence alignment. that's the whole name section. short, sweet, iconic.

🦋 SYNOPSIS 🦋

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

so you hand it your options, then the conf directory, then a FASTA file, and optionally a FASTA output file. the last one's optional, the first two are not, no cap. 🎀

💖 DESCRIPTION 💖

DIALIGN-TX is an improved algorithm for segment-based multiple protein alignments. periodt.

here's the tea: DIALIGN-TX is a complete reimplementation of the segment-base approach, and it brings a whole bunch of new improvements and heuristics that significantly enhance the quality of the output alignments compared to DIALIGN 2.2. and this significant superiority? it's been observed on local benchmarks and on global alignment benchmarks. so like, not just one vibe. both vibes. 👑

✨ OPTIONS ✨

  • -d — Debug-Mode [DEFAULT 0] 🐛
    • 0 no debug statements
    • 1 debugs the current phase of the processing
    • 2 very loquacious debugging (she talks a LOT)
    • 5 hardcore debugging (absolutely unhinged, we love her)
  • -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]. (yes bestie, -m shows up twice in this list — that's exactly how the original page has it, and I'm not about to edit the source material. 🙈)
  • -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. (hi hello, here's the help, you're welcome 🫶)

🎀 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. so like, that first positional arg? this is her. 🌈

💜 SEE ALSO 💜

DIALIGN-TX is a re-implementation of dialign2-2(1). (See http://dialign.gobics.de/ for more information about DIALIGN2). iykyk.

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 © 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.

and that's the whole page, bestie!! 💖 this manual is dialign-tx 1.0.2, dated 12/15/2008, and it lives in section 1 of the manual — so go forth, align your segments, and be the main character of your own multiple sequence alignment. mwah. 💅🦋🌸

📦 where this page comes from