DIALIGN(1)

📦 version 2.2.1, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking

🌸 DIALIGN — like, the manual page 💅

ok bestie so this is the manpage for DIALIGN (the binary you'll actually be running is dialign2-2), and I'm about to walk you through every single flag like it's a group chat and you're my favourite person. grab a drink. we're doing this. 🫶

✨ NAME ✨

dialign2-2 — the multiple alignment program that does the whole segment-to-segment thing. that's the vibe. that's the whole personality. 💫

✨ SYNOPSIS ✨

dialign2-2 [options] [seq_file]

seq_file is the name of your input sequence file, and lowkey important detail: it has to be a multiple FASTA file — meaning all your sequences live together in that one single file. no splitting them up, bestie. one file, many sequences, that's the rule. 💖

✨ DESCRIPTION ✨

so dialign2-2 builds alignments out of gapfree pairs of similar segments of your sequences. that's the whole magic trick — segment against segment, no gaps inside the pieces themselves.

and here's the part that's genuinely giving genius: if you're aligning nucleic acid sequences that might (or might not!) be coding, DIALIGN can optionally translate the compared nucleic acid segments´ into peptide segments´ according to the genetic code. and it does this without presupposing any of the three possible reading frames — so literally all combinations of reading frames get checked for significant similarity. no assumptions, no shortcuts, just thorough. slay. 🔥

by default, DIALIGN creates a single file containing:

  • an alignment of the input sequences in DIALIGN format.
  • that same alignment in FASTA format.
  • a sequence tree in PHYLIP format. this tree gets built by applying the UPGMA clustering method to the DIALIGN similarity scores. it roughly reflects the different degrees of similarity among your sequences. and ngl, if you want real, detailed phylogenetic analysis, please go use the usual methods for phylogenetic reconstruction — this tree is a vibe check, not a phylogeny paper. 🌳

the format of the output files is documented in /usr/share/doc/dialign/USER_GUIDE.gz. and if you want it, the FASTA, CLUSTALW and MSF output formats are optionally available too — check OPTIONS below, bestie. 📚

✨ OPTIONS ✨

okay here's the whole menu. every single one. no skips. 👑

  • -afc — creates an additional output file "*.afc" containing data of all fragments considered for alignment. > WARNING: this file can be HUGE! like, actually huge. 💀
  • -afc_v — like -afc but verbose: fragments are explicitly printed. > WARNING: this file can be EVEN BIGGER! bestie I am not joking. 😭
  • -anc — anchored alignment. requires a file seq_file.anc containing anchor points. 📌
  • -cs — if segments get translated, then not only the Watson strand´ but also the Crick strand´ gets looked at. both strands, double the checking. 🧬
  • -cw — additional output file in CLUSTAL W format.
  • -ds — `DNA alignment speed up´. non-translated nucleic acid fragments are only taken into account if they start with at least two matches. so yes, it speeds up DNA alignment — but at the expense of sensitivity. trade-off queen. ⚡
  • -fa — additional output file in FASTA format.
  • -ff — creates file *.frg containing information about all fragments that are part of the respective optimal pairwise alignments, plus information about consistency in the multiple alignment. 🗂️
  • -fn out_file — output files get named out_file.extension.
  • -fop — creates file *.fop containing coordinates of all fragments that are part of the respective pairwise alignments. 📍
  • -fsm — creates file *.fsm containing coordinates of all fragments that are part of the final alignment. 🎯
  • -iw — overlap weights switched off. (by default, overlap weights are used if up to 35 sequences are aligned.) this option speeds up the alignment but may lead to reduced alignment quality. you win time, you might lose quality. your call. ⏱️
  • -lgs — Long genomic sequences´. this one is a combo meal, it combines the following options: -ma, -thr 2, -lmax 30, -smin 8, -nta, -ff, -fop, -ff, -cs, -ds, -pst. (yes, -ff` is in there twice. that's just how it is, bestie, I don't make the rules.) 🍱
  • -lgs_t — like -lgs but with all segment pairs assessed at the peptide level (rather than the ´mixed alignments´ you get with the -lgs option). therefore faster than -lgs but not very sensitive for non-coding regions. speed demon, but it has a blind spot. 🏃♀️
  • -lmax x — maximum fragment length = x. (default: x = 40, or x = 120 for `translated´ fragments.) a shorter x speeds up the program but may affect alignment quality. 📏
  • -lo — (Long Output) additional file *.log with information about fragments selected for pairwise alignment and about consistency in the multi-alignment procedure. 📝
  • -ma — `mixed alignments´ consisting of P-fragments and N-fragments, when nucleic acid sequences are aligned. 🧪
  • -mask — residues not belonging to selected fragments get replaced by * characters in the output alignment (instead of being printed in lower-case characters). ✳️
  • -mat — creates file *mat with substitution counts derived from the fragments that have been selected for alignment. 🔢
  • -mat_thr t — like -mat but only fragments with weight score > t are considered. 🎚️
  • -max_link — "Maximum linkage" clustering is used to construct the sequence tree (instead of UPGMA). 🌲
  • -min_link — "Minimum linkage" clustering is used. 🌱
  • -mot — "Motif" option. 🎀
  • -msf — separate output file in MSF format.
  • -n — input sequences are nucleic acid sequences. no translation of fragments. 🚫🧬
  • -nt — input sequences are nucleic acid sequences, and nucleic acid segments´ are translated to peptide segments´. 🔁
  • -nta — No textual alignment´. the textual alignment is suppressed. this option makes sense if other output files are what you're actually interested in — e.g. the fragment files created with -ff, -fop, -fsmor-lo`. 🙈
  • -o — fast version. resulting alignments may be slightly different. 🏎️
  • -ow — overlap weights enforced. (by default, overlap weights are used only if up to 35 sequences are aligned, since calculating overlap weights is time consuming.) > Warning: overlap weights generally improve alignment quality, but the running time increases in the order O(n^4) with the number of sequences. this is exactly why, by default, overlap weights are used only for sequence sets with < 36 sequences. ⚠️
  • -pst — "Print status". creates and updates a file *.sta with information about the current status of the program run. this one is recommended if you're aligning large data sets, because it lets you estimate the remaining running time. very much a "how long is this going to take" feature. ⌛
  • -smin x — minimum similarity value for the first residue pair (or codon pair) in fragments. speeds up protein alignment or alignment of translated DNA fragments, at the expense of sensitivity. ⚖️
  • -stars x — maximum number of * characters indicating degree of local similarity among sequences. by default, no stars are used, and numbers between 0 and 9 are printed instead. ⭐
  • -stdo — results written to standard output. 📤
  • -ta — standard textual alignment printed (this overrides the suppression of textual alignments in special options, e.g. -lgs). 📄
  • -thr x — threshold T = x. 🎯
  • -xfr — "Exclude fragments". you can specify a list of fragments that are NOT considered for pairwise alignment. 🙅♀️
General remark, bestie, this one matters: if you use contradictory options, the subsequent options override the previous ones. like:
dialign2-2 -nt -n seq_file

runs the program with the -n option (no translation!), while

dialign2-2 -n -nt seq_file

runs it with the -nt option (translation!). order matters. last one standing wins. 👑

✨ SEE ALSO ✨

✨ ENVIRONMENT VARIABLES ✨

you can create an environment variable `DIALIGN2_DIR´ pointing to a directory where the substitution matrices are (see FILES below). but here's the chill part: when DIALIGN is installed from the Debian package, you do not need to set this environment variable to run DIALIGN. it just works. 🫶

✨ FILES ✨

DIALIGN2 needs these files: tp400_dna, tp400_prot, tp400_trans and BLOSUM. when DIALIGN is installed from the Debian package, they're stored in /usr/share/dialign/. 📁

DIALIGN 2 uses the BLOSUM62 amino acid substitution matrix. and in the current version, it is NOT possible to replace BLOSUM62 with other similarity matrices. so don't even try it, bestie, that door is closed. 🚪

✨ REFERENCE ✨

B. Morgenstern (1999). DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment. Bioinformatics 15, 211 - 218.

and listen — public research assisted by DIALIGN should cite this article. if this tool carried your paper, you cite it. that's the deal. 📚💖

✨ AUTHORS ✨

  • Burkhard Morgenstern <bmorgen@gwdg.de> — author of DIALIGN
  • Said Abdeddaim — author of DIALIGN
  • Charles Plessy <plessy@debian.org> — wrote this manpage

DIALIGN was written by Burkhard Morgenstern and Said Abdeddaim at University of Bielefeld (FSPM and International Graduate School in Bioinformatics and Genome Research), GSF (ISG, IBB, MIPS/IBI), North Carolina State University, Universite de Rouen, MPI fuer Biochemie (Martinsried), University of Goettingen, Institute of Microbiology and Genetics.

this manual page was adapted from the DIALIGN manual by Charles Plessy <plessy@debian.org> for the Debian system (but may be used by others). permission is granted to copy, distribute and/or modify this document under the terms of the GNU Lesser General Public License, Version 2.1 any later version published by the Free Software Foundation.

on Debian systems, the complete text of the GNU Lesser General Public License can be found in /usr/share/common-licenses/LGPL. 📜

Copyright © 1999 Burkhard Morgenstern (for DIALIGN) Copyright © 2006, 2007, 2008 Charles Plessy (for this manpage)

and that's the whole page, bestie!! this was dialign2-2 version 2.2.1, dated avril 9, 2006, living in section 1 of the manual like the icon it is. go align something gorgeous. 💅✨🦋

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