HMM_VIEW(1)

💖 HMM_VIEW(1) — the manual, but make it cute 💖

okay so bestie, welcome to hmm_view, a User Command, and she is literally the moment. 🎀

✨ NAME ✨

hmm_view — produces a graphical description of the state-transition

🌸 DESCRIPTION 🌸

so what she does is: she produces a graphical description of the state-transition structure of a phylo-HMM. 🦋

and then — and this is the iconic part — that output can be converted into an actual viewable image using the dot program. no cap. the plug is right here: http://www.graphviz.org 👑

so like… you get the graph, dot makes it pretty, you stare at it, you understand your phylo-HMM. main character pipeline fr fr. 💅

⭐ SYNOPSIS ⭐

hmm_view [OPTIONS] <hmm_fname> <cat_map_fname>|<cat_map_str>

yes she takes a filename or a literal string for the category map, pick your fighter 💀

💜 OPTIONS 💜

• -k <nrcats> — assume a separate version of each state for each of <nrcats> rate categories. one state, many glow-ups 🌈
• -i <icats> — assume use of the indel model for the specified category names. 🧚
• -t <tree> — (Required with -i) the tree topology to assume for the indel model, as a .nh file. like, if you're doing -i you have to bring the tree too, no exceptions bestie 🫶
• -C <cats> — show only the states corresponding to the specified category names. filtering! we love a curated feed ✨
• -R <piv> — reflect the HMM about the specified 'pivot' categories. (Not yet implemented.) so like… she's on the moodboard but she is NOT coming to the party 😭
• -x — don't show unconnected states. ghost them. 💀

ngl -R is giving "coming soon" and by coming soon we mean not implemented, so don't go building your whole workflow on it, okay? 🥺

💫 one last thing 💫

this whole page is hmm_view 1.4, dated May 2016, and it's filed under User Commands like the legend she is. thanks for coming to my TED talk, go make some beautiful graphs, ily, bye 💖🦋✨🌸👑