hmm2align(1)

💖 hmm2align(1) — HMMER Manual, section 1 💖

okay so bestie, welcome to hmm2align(1) from the HMMER manual, section 1. this is the one that takes your profile HMM and your sequences and ✨ makes them a multiple sequence alignment ✨. no cap.

🌸 SYNOPSIS 🌸

hmm2align [options] hmm2file seqfile

🦋 DESCRIPTION 🦋

so here's the vibe: hmm2align reads an HMM file (it's called hmmfile down in the prose, hmm2file up in the synopsis — she contains multitudes 💅) and a set of sequences from seqfile, aligns those sequences to the profile HMM, and outputs a multiple sequence alignment. that's the whole job. main character behavior.

seqfile can be in any unaligned or aligned file format that HMMER accepts. and listen — if it is in a multiple alignment format (think Stockholm, MSF, SELEX, ClustalW), the existing alignment gets ignored. like, the sequences are read as if they were unaligned, and hmm2align will align them the way it wants. it's giving "i'm the one in charge here." periodt.

✨ OPTIONS ✨

• -h — print brief help, and bestie it includes the version number plus a summary of all the options, even the expert ones. so you never have to guess.
• -m — only include in the alignment those symbols that are aligned to match states. symbols assigned to insert states? not shown. they're not on the guest list. 🙈
• -o <f> — save the alignment to file <f> instead of to standard output.
• -q — quiet mode: suppress all output except the alignment itself. super useful for piping or redirecting the output. chef's kiss for scripts. 🔥

👑 EXPERT OPTIONS 👑

• --informat <s> — assert that the input seqfile is in format <s>, and do not run Babelfish format autodection (yep, "autodection," that's how it's spelled, we don't fix the source code, we respect it 💜). this makes the program a little more reliable, because the Babelfish can make mistakes. highly recommended for unattended, high-throughput runs of HMMER. valid format strings include FASTA, GENBANK, EMBL, GCG, PIR, STOCKHOLM, SELEX, MSF, CLUSTAL, and PHYLIP. see the User's Guide for a complete list.
• --mapali <f> — reads an alignment from file <f> and aligns it as a single object to the HMM; i.e. the alignment in <f> is held fixed. this lets you align sequences to a model with hmm2align and view them in the context of an existing trusted multiple alignment. the alignment-to-the-alignment is defined by a "map" kept in the HMM, so it's fast and guaranteed to be consistent with the way the HMM was constructed from the alignment. the alignment in the file <f> must be exactly the alignment that the HMM was built from. compare the --withali option.
• --oneline — output the alignment with one line per sequence instead of interleaving the sequence alignment blocks. only affects Stockholm format output. lowkey a glow-up for readability.
• --outformat <s> — output the alignment in format <s>. the default is Stockholm format. valid formats include Stockholm, SELEX, MSF, Clustal, Phylip, and A2M.
• --withali <f> — reads an alignment from file <f> and aligns it as a single object to the HMM; i.e. the alignment in <f> is held fixed. same deal as above: align sequences to a model with hmm2align and view them in the context of an existing trusted multiple alignment. but — the alignment to the alignment is done with a heuristic (nonoptimal) dynamic programming procedure, which may be somewhat slow and is not guaranteed to be completely consistent with the way the HMM was constructed (though it should be quite close). the tradeoff? any alignment can be used, not just the alignment that the HMM was built from. compare the --mapali option. choose your fighter. 💅

🌈 SEE ALSO 🌈

Master man page, with full list of and guide to the individual man pages: see hmmer2(1).

For complete documentation, see the user guide (ftp://selab.janelia.org/pub/software/hmmer/2.3.2/Userguide.pdf); or see the HMMER web page, http://hmmer.janelia.org/.

🎀 COPYRIGHT 🎀

Copyright (C) 1992-2003 HHMI/Washington University School of Medicine.

Freely distributed under the GNU General Public License (GPL). See the file COPYING in your distribution for details on redistribution conditions.

🫶 AUTHOR 🫶

Sean Eddy HHMI/Dept. of Genetics Washington Univ. School of Medicine 4566 Scott Ave. St Louis, MO 63110 USA http://www.genetics.wustl.edu/eddy/

and that's the whole page bestie, every flag, every file, every address, nothing skipped, iykyk 💖

okay so final sign-off: this was HMMER 2.3.2, dated Oct 2003, page hmm2align(1). iconic, legendary, aligned. slay 💅✨🌸