GAPCLEANER(1)

💖 GAPCLEANER 💖

okay bestie, buckle up, because this little tool is lowkey iconic 💅 it's called gapcleaner, it lives in the FSA fam, and it's here to sort out your indels. yes, those indels. the gap drama. we're fixing it. periodt ✨

✨ NAME ✨

gapcleaner — find the most-parsimonious ordering of indels 🦋

like, the most parsimonious one. not just any ordering. the slay ordering. iykyk.

🎀 SYNOPSIS 🎀

gapcleaner <multi-FASTA or Stockholm alignment>

that's it. that's the whole vibe. you hand it an alignment, it does its thing 🌸

👑 DESCRIPTION 👑

gapcleaner comes from FSA 1.15.9, no cap 🫶

so what does it actually do, you ask? it finds the most-parsimonious ordering of indels. fr fr. what that means in practice is it finds the minimal chain decomposition of the POSET of the alignment — and the way that works out is it minimizes the number of gap-openings across the sequences. it's giving graph theory main character energy and honestly? we're obsessed 💀✨

🚨 heads up bestie: your input protein alignment must be in multi-FASTA or Stockholm format. no other formats. don't try it. the vibe check will fail 🙈

💜 AUTHOR 💜

this manpage was written by Andreas Tille for the Debian distribution, and it can be used for any other usage of the program. king behavior honestly 👑

and that's the whole page, bestie!! gapcleaner 1.15.9, dating all the way back to December 2015 — a true vintage queen 👑💖 go minimize those gap-openings, you got this 🌈⭐