hmm2convert(1)

📦 version 2.3.2, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking

💖 hmm2convert(1) — the HMMER Manual glow-up ✨

okay bestie, welcome to hmm2convert from the HMMER manual, and no cap this one is a lil format-switcher and it's lowkey iconic 💅

✨ NAME ✨

hmm2convert — convert between profile HMM file formats 🦋

🌸 SYNOPSIS 🌸

hmm2convert [options] oldhmmfile newhmmfile

💜 DESCRIPTION 💜

So here's the tea, bestie: hmm2convert reads an HMM file from oldhmmfile in any HMMER format, and writes it out to newhmmfile in a new format. It's giving glow-up, it's giving rebrand 🎀

🚨 REAL TALK: oldhmmfile and newhmmfile must be different files. You can't reliably overwrite the old file. Do not try it. Not me watching you try it 🙈

By default, the new HMM file is written in HMMER 2 ASCII format.

The available formats are:

  • HMMER 2 ASCII — the default, the moment, the standard 💖
  • HMMER 2 binary — via -b
  • GCG profile — via -p
  • Compugen XSW extended profile — via -P

💅 OPTIONS 💅

  • -a — Convert to HMMER 2 ASCII file. This is literally the default, so this option is unnecessary. Like, it's cute, but you don't need it 🫶
  • -b — Convert to HMMER 2 binary file. Binary era 🔥
  • -h — Print brief help; includes the version number and a summary of all the options, including the expert options. The lore drop 📖✨
  • -p — Convert to GCG profile .prf format.
  • -A — Append mode; append to newhmmfile rather than creating a new file.
  • -F — Force; if newhmmfile already exists, and -A is not being used to append to the file, hmm2convert will refuse to clobber the existing file unless -F is used. She's protective of your files, and honestly? Valid 💀
  • -P — Convert the HMM to Compugen XSW extended profile format, which is similar to GCG profile format but has two extra columns for delete-open and delete-extend costs. (I do not believe that Compugen publicly supports this format; it may be undocumented.) 👀

🔍 SEE ALSO 🔍

  • Master man page, with the full list of and guide to the individual man pages: see hmmer2(1). The mothership 👑
  • 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/. Go read, bestie, it's giving education 🌈

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. Legal girlies stay winning ⭐

👑 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/

okay that's the whole page, you ate that 💖✨🎀🦋

this was HMMER 2.3.2, dated Oct 2003, and the page is hmm2convert(1) — mwah, go convert something gorgeous, bestie 💅🌸

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