BP_RUN_PROTDIST(1p)

💖 NAME 💖

okay so bestie, this page is BP_RUN_PROTDIST(1p) — a lil' slice of User Contributed Perl Documentation — and what it's actually called in the NAME line is run_neighbor (yes really, that's what it says, we're keeping it exactly like that, no cap) and its whole deal is: run Phylip's 'protdist' program through Bioperl. 🦋

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✨ SYNOPSIS ✨

run_protdist [-i inputfile] [-o outfilename]

that's it, that's the whole vibe check 💅

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🌸 DESCRIPTION 🌸

so you hand it an alignment file and it runs protdist on it. the file has to be named either .aln or .phy — and no, that's not me being picky, it's literally required, because that's how the script figures out whether it needs to convert a clustalw alignment into phylip format. 🔥

and hey, you are totally welcome to extend the script so it works on other MSA formats that bioperl supports. this thing is intended for very simple manual pipelines, like, it's not out here trying to be a whole framework. it's just a girl doing her job. 🎀

📌 the input file should be named in the form of file.phy or file.aln — the program expects a file in the form of (\S+)\.(\S+). like, it's pattern-matching your filename, so name it right or it's giving confused. 😭

this runs the application 'protdist' using the 'KIMURA' formula to build a protein distance matrix. and if you're on phylip3.6 and you wanna use JTT instead, you're gonna want to make some changes yourself. 🫶 the author says they're happy to help add that in as a cmd-line argument if it gets requested — so like, ask and you shall receive, bestie. 👑

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👑 AUTHOR 👑

Jason Stajich, jason-AT-open-bio-DOT-org — shoutout to the icon who wrote this, we love her fr fr 💜

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🌈 okay that's the whole page! this was rendered from perl v5.36.0, dated 2023-01-22, and the page itself is BP_RUN_PROTDIST(1p). mwah, go run some protdist, you got this 💅✨🧚