hmmlogo(1)

📦
version 3.4 · 2 versions
, in debian trixie, nixos 26.05, nixpkgs unstable, ubuntu noble, ubuntu resolute, ubuntu stonking

💖 hmmlogo — the manual page, but make it cute

okay bestie, so this is hmmlogo(1) from the HMMER Manual, and it is genuinely one of the slayest little tools in the whole package. let's get into it 💅

✨ NAME ✨

hmmlogo — produce a conservation logo graphic from a profile 🎀

✨ SYNOPSIS ✨

hmmlogo [options] hmmfile

🌸 DESCRIPTION 🌸

so basically, hmmlogo computes letter height and indel parameters that you can use to produce a profile HMM logo. it's giving "logo girlie". 🦋

lowkey the tea here is that this tool is essentially a command-line interface for a whole bunch of the data that sits underneath the Skylign logo server (skylign.org). iykyk ✨

by default, hmmlogo prints out a table of per-position letter heights (and which heights you get depends on the height method you asked for, bestie), and then it prints out a table of per-position gap probabilities. two tables, one vibe. 💅

and for the visual learners: in a typical logo, the total height of a stack of letters for one position depends on the information content of that position, and that stack height gets subdivided according to the emission probabilities of the letters of the alphabet. stack 'em up, subdivide 'em, periodt. 👑

💅 OPTIONS 💅

  • -h — help bestie!! prints a brief lil reminder of command line usage plus all the available options. no gatekeeping here 🫶
  • --height_relent_all — total height = relative entropy (aka information content), and all the letters get a positive height. this one is the default, so if you don't say anything, this is the vibe you're getting ⭐
  • --height_relent_abovebg — total height = relative entropy (aka information content) again, but this time only letters with above-background probability get a positive height. if you're below background, you get nothing. sorry babe 😭
  • --height_score — total height = the sums of scores of positive-scoring letters, so a letter's height depends on the score of that letter at that position. and again, only letters with above-background probability (i.e. a positive score) get a positive height. ⚠️ heads up though: with this method, only letter height is meaningful — stack height has no inherent meaning at all. do not come for the stack, it has nothing to say fr fr 💀
  • --no_indel — don't print out the indel probability table. if you only want the one table, this is your girl 🙈

🌈 SEE ALSO 🌈

  • see hmmer(1) for a master man page with a list of all the individual man pages for programs in the HMMER package. it's the group chat of man pages 💖
  • for complete documentation, see the user guide that came with your HMMER distribution (Userguide.pdf); or see the HMMER web page (http://hmmer.org/). ✨

Copyright (C) 2023 Howard Hughes Medical Institute. Freely distributed under the BSD open source license.

for additional info on copyright and licensing, see the file called COPYRIGHT in your HMMER source distribution, or see the HMMER web page (http://hmmer.org/). 🫶

🦋 AUTHOR 🦋

http://eddylab.org

and that's the whole page bestie!! this one is from HMMER 3.4, dated Aug 2023 — so yeah, she's iconic, she's giving main character energy, and she's been serving logos since day one. go make something beautiful 💖✨🎀

📦 where this page comes from