INDELFIT(1)

✨ INDELFIT — the girlies are modeling indels ✨

okay so bestie, welcome to indelFit (that's section 1 of the manual, iykyk) 💅 she lives in the User Commands girlie ecosystem and she has ONE job: figuring out the parameters of a simple indel model when you already know the indel history. no cap.

🌸 NAME 🌸

indelFit — estimate the parameters of a simple indel model, given an indel history. literally that's the whole thing. she's focused. she's booked. she's serving parameter estimation. 💖

🦋 DESCRIPTION 🦋

So here's the vibe: you hand indelFit an indel history and a tree, and she estimates the parameters of a simple indel model for you. no drama, no fuss. 🎀

By default (and this is the important part, don't skip it) she writes estimates of three parameters to stdout:

• an insertion rate alpha 🌱
• a deletion rate beta 🍂
• a parameter tau ✨ which is roughly equal to the inverse of the expected indel length — modulo the adjustments required to make the probabilities sum to one, bestie, we don't make the rules

Not me explaining where you even get these inputs: an indel history can be obtained with indelHistory, and a tree with phyloFit. 🫶

💅 OPTIONS 💅

• --alpha, -a <val> — starting value of alpha, the insertion rate. default is 0.02. 🌱
• --beta, -b <val> — starting value of beta, the deletion rate. default is 0.04. 🍂
• --tau, -t <val> — starting value of tau, the length parameter. default is 0.05. ✨
• --lnl, -L — compute the log likelihood of the model only, without optimizing any parameters. the options above can be used to set the parameters as desired. it's giving "just tell me the score, don't touch anything" 😌
• --columns, -c — output the log likelihood of each column. every single one. she's thorough like that. 📊
• --features, -f <file.gff> — estimate separate parameters for each type of feature in the given file, as well as for background sites. slay, segmentation queen 👑
• --reference, -r <name> — (for use with --features) name of species (node of tree) defining the coordinate frame of features. by default, the coordinate frame of the entire alignment is assumed. 🧭
• --log, -l <file> — write the log of the optimization to the specified file. receipts, bestie, always keep the receipts 🧾
• --help, -h — display this help message and exit. the classic. the icon. the moment. 🫶

and that's the whole page, angel 💜 go forth and estimate those rates, the model believes in you 🌈⭐🧚

this was indelFit version 1.4, dated May 2016 — yeah she's a little vintage, but vintage is a vibe, and she still eats 💖