HMM_TWEAK(1)

💖 HMM_TWEAK(1) 💖

okay bestie, gather round, because this one is so niche and so powerful. it's hmm_tweak, a User Commands classic, and she's here to mess with your HMM definition files (respectfully).

✨ NAME ✨

hmm_tweak — Alter transition probabilities in an HMM definition file. 💅

🌸 DESCRIPTION 🌸

So what she does is: alter transition probabilities in an HMM definition file. that's the whole gig, no cap.

Here's the tea tho — after the operations you specified get performed, the transition probabilities get renormalized (gotta keep them valid, queen) and the adjusted file is written to standard out. and the best part? this program may be used multiple times in a pipe. chain her up, she loves it. 🫶

🦋 USAGE 🦋

hmm_tweak [OPTIONS] <file.hmm> <cmap.cm>

🎀 OPTIONS 🎀

• -f <cats> — Operate on transitions from states corresponding to the specified category names (default all). 💖
• -t <cats> — Operate on transitions to states corresponding to the specified category names (default all). 💖
• -m <fact> — Multiply transition probabilities by the specified factor. math era. ✨
• -a <const> — Add the specified constant to transition probabilities.
• -e <val> — Set transition probabilities equal to the specified value. just straight up assign it, periodt.
• -i <icats> — Assume a phylo-HMM indel model for states corresponding to the specified category names.
• -u <tree> — (Required with -i) Assume given tree topology (.nh file). yes bestie, it's mandatory, don't skip it.
• -F <gps> — (For use with -i) Operate on transitions from states corresponding to the specified gap-pattern numbers (ANDed with -f).
• -T <gps> — (For use with -i) Operate on transitions to states corresponding to the specified gap-pattern numbers (ANDed with -t).
• -z — Equalize transition probabilities. Sets all transition probabilities indicated by -f/-t/-F/-T to their overall average value. Options -m and/or -a can be used to adjust this average value. glow-up mode. 👑
• -R — Restrict to successive transitions within a category range.
• -y — Like -z, except it computes separate averages for five classes of transitions, based on the gap patterns of the states involved:
  • between null gap patterns,
  • between equal non-null gap patterns,
  • from null to non-null gap patterns,
  • from non-null to null gap patterns,
  • and all others.

Useful with the indel model when training data is sparse (e.g., for splice-site states). Options -m and -a will be applied to transitions of the 3rd and 5th classes described. iykyk. 🧚

• -h — Print this help message. the classic. 🌈

ngl bestie, if you're out here flipping transition probabilities without thinking about renormalization, that's a vibe check you're failing. she handles it for you, but know that it's happening. 💀

that's the whole page, my love. this gorgeous thing is hmm_tweak version 1.4, and she's been serving since May 2016. 💜✨🎀