POA(1)

📦 version 2.0+20060928, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking

💖 poa(1) — the manual page, but make it slay 💖

okay bestie, so this is the man page for poa, and no cap, it's a whole vibe. it lives in section 1 of the manual (that's the (1) up there, she's iconic like that). let's get into it 💅

✨ NAME ✨

poa — align a set of sequences or alignments. that's it, that's the job, and she does it beautifully 🦋

✨ SYNOPSIS ✨

poa [OPTIONS] [MATRIXFILE]

okay so important thing, and I need you to hear me on this one: one of the -read_fasta, -read_msa, or -read_msa_list arguments MUST be used, because a sequence or alignment file is literally required. you can't just show up empty-handed, that's not the energy ✋

✨ DESCRIPTION ✨

POA is Partial Order Alignment, a fast program for multiple sequence alignment (MSA) in bioinformatics. her whole thing? speed, scalability, sensitivity, and the superior ability to handle branching / indels in the alignment. it's giving main character energy, fr fr 👑

Partial order alignment is an approach to MSA, and the way that it can be combined with existing methods such as progressive alignment?? obsessed. POA optimally aligns a pair of MSAs, which therefore can be applied directly to progressive alignment methods such as CLUSTAL. and for large alignments, Progressive POA is 10 to 30 times faster than CLUSTALW. ten to thirty. times. faster. no cap 🔥

🌸 EXAMPLES 🌸

here's the moment you've been waiting for, the demo:

poa -read_fasta multidom.seq -clustal m.aln blosum80.mat

and if you're on Debian, bestie, you can test poa with this command right here:

poa -read_fasta /usr/share/doc/poa/examples/multidom.seq -clustal /dev/stdout -v /usr/share/poa/blosum80.mat

go ahead, run it, I'll wait 🫶

👑 OPTIONS 👑

💜 INPUT 💜

  • -read_fasta FILE — read in a FASTA sequence file. the classic. the starter pack. 🌱
  • -read_msa FILE — read in an MSA alignment file.
  • -read_msa2 FILE — read in a second MSA file. two of them. a duo. 💞
  • -subset FILE — filter the MSA to include the list of seqs in the file.
  • -subset2 FILE — filter the second MSA to include the list of seqs in the file.
  • -remove FILE — filter the MSA to include the list of seqs in the file.
  • -remove2 FILE — filter the second MSA to include the list of seqs in the file.
  • -read_msa_list FILE — read an MSA from each filename listed in the file. a lil reading list, cute 📚
  • -tolower — force FASTA/MSA sequences to lowercase (nucleotides in our matrix files).
  • -toupper — force FASTA/MSA sequences to UPPERCASE (amino acids in our matrix files). she's loud and she's proud 📣

💜 ALIGNMENT 💜

  • -do_global — do global alignment.
  • -do_progressive — perform progressive alignment using a guide tree built by neighbor joining from a set of sequence-sequence similarity scores.
  • -read_pairscores FILE — read a tab-delimited file of similarity scores (if not provided, scores are constructed using pairwise sequence alignment).
  • -fuse_all — fuse identical letters on align rings. merging the girlies 💫

💜 ANALYSIS 💜

  • -hb — perform heaviest bundling to generate consensi.
  • -hbmin VALUE — include in the heaviest bundle sequences with percent ID (as a fraction) >= VALUE.

💜 OUTPUT 💜

  • -pir FILE — write out the MSA in PIR format.
  • -clustal FILE — write out the MSA in CLUSTAL format.
  • -po FILE — write out the MSA in PO format.
  • -preserve_seqorder — write out the MSA with sequences in their input order. keeping it in order, as she should 🎀
  • -printmatrix LETTERS — print the score matrix to stdout.
  • -best — restrict MSA output to heaviest bundles (PIR only).
  • -v — run in verbose mode (e.g. output gap penalties). she's telling you everything 💀

🌈 REFERENCE 🌈

please cite this, bestie, it's the polite thing to do:

Grasso C, Lee C. (2004) Combining partial order alignment and progressive multiple sequence alignment increases alignment speed and scalability to very large alignment problems. Bioinformatics. 2004 Jul 10;20(10):1546-56. Epub 2004 Feb 12.

🦋 SEE ALSO 🦋

the homepage of POA is http://www.bioinformatics.ucla.edu/poa — go say hi 💖

⭐ COPYRIGHTS ⭐

Copyright (C) 2001, 2006 Christopher Lee <leec@mbi.ucla.edu>. POA is free software. You can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation.

this manual page was written by Charles Plessy <charles-debian-nospam@plessy.org> for the Debian(TM) system (but may be used by others). Permission is granted to copy, distribute and/or modify this document under the terms of the GNU General Public License, Version 2 any later version published by the Free Software Foundation.

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

Copyright © 2006 Charles Plessy

and that's the whole page, bestie 💅 this manual page was dated september 26, 2006 — yeah, she's vintage, she's a classic, she predates the whole timeline and she's still out here aligning sequences. periodt. 🎀✨🦋

📦 where this page comes from