INDELHISTORY(1)

💅 INDELHISTORY — bestie, let's get you an indel history 💅

okay so welcome to indelHistory, a User Command, and honestly? she's giving "quiet little tool that does exactly one thing and does it slay." Let's go. 🦋

✨ NAME ✨

indelHistory — obtain an "indel history" for an alignment and write it to a file. no cap, that's literally the whole job. 💖

🌸 DESCRIPTION 🌸

So what she does is: you hand her an alignment, and she hands you back an "indel history" written to a file, describing all the insertions and deletions across every species, in a cute compact format. lowkey iconic.

Now here's the tea, because there are two whole vibes depending on what your alignment contains ☕:

• If your alignment has sequences for only the leaves of the tree you specified, then the indel history gets inferred using a simple parsimony algorithm. she's doing detective work. 🕵️‍♀️
• If your alignment has sequences for all the nodes in the tree, then the indel history is simply extracted from the file. no guessing needed, it's already right there, periodt. 👑

🎀 OPTIONS 🎀

• --msa-format, -i FASTA|MAF|SS|.... — read the alignment in whichever file format you name here. the default is FASTA, so if you don't say anything she just assumes FASTA. 💅
• --output-alignment, -A — instead of just a lil summary of indels, she outputs an alignment in FASTA format containing sequences for all ancestral and leaf nodes. glow-up mode: everybody's invited to the party. 🫶
• --read-history, -H <fname> — read an indel history directly from the file you specify. it's useful for debugging. ngl this one's a bit of a rule-breaker because the alignment and tree arguments are not required here;

however, if an alignment is given alongside --read-history and --output-alignment, then actual bases can be output for leaf species. so like, she'll fill in the real letters for the leaves. ✨

• --ia-names, -I — assume the ancestral sequences in alignment.fa are named using the convention from Mathieu Blanchette's inferAncestors program. for example, "RAT+MOUSE+RABBIT+" is the name for the last common ancestor of "rat", "mouse", and "rabbit". yes the plus signs are doing a lot of work and yes they ate. 💀
• --help, -h — display this help message. she's happy to explain herself. 😭

🌈 quick vibe check: if you want the indel history inferred, give her leaves only. if you want it extracted, give her every node. don't mix those up bestie, that's the whole plot twist. 🔥

and that's the page, babe 💜 this was indelHistory version 1.4, dated May 2016 — shoutout to the source/version and that lil date stamp, we love a well-documented era. now go run it and be the main character of your own phylogeny. 👑💖✨