PRODY(1)

✨ PRODY(1) ✨

okay so this is PRODY(1), a User Commands page, and bestie we are about to get into it 💅

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💖 NAME 💖

ProDy — Sequence Evolution and Dynamics Analysis. that's it, that's the whole name section, slay ✨

🌸 DESCRIPTION 🌸

so the usage is literally this, verbatim, no edits:

usage: evol [-h] [-c] [-v] [-e]
            {search,fetch,filter,refine,merge,occupancy,conserv,coevol,rankorder}
            ...

Evol: Sequence Evolution and Dynamics Analysis — that's the whole vibe of the tool, periodt 🦋

🎀 options 🎀

• -h, --help — shows this help message and dips. iconic behaviour honestly 👑
• -c, --cite — prints the citation info and exits. cite your sources bestie, it's giving academic integrity 💜
• -v, --version — prints the ProDy version and exits 🫶
• -e, --examples — shows usage examples and exits. yes ma'am, demo mode 🔥

💫 subcommands 💫

the lineup is literally:

{search,fetch,filter,refine,merge,occupancy,conserv,coevol,rankorder}

and here's what each one does, no gatekeeping:

• search — search Pfam with given query 🔍
• fetch — fetch MSA files from Pfam 📥
• filter — filter an MSA using sequence labels 🌈
• refine — refine an MSA by removing gapped rows/colums 🧚 (yes it says "colums", we're keeping it exactly as it is, no cap)
• merge — merge multiple MSAs based on common labels 🫶
• occupancy — calculate occupancy of rows and columns in MSA 📊
• conserv — analyze conservation using Shannon entropy ⭐
• coevol — analyze co-evolution using mutual information 🔥
• rankorder — identify highly coevolving pairs of residues 👑

ngl if you need the tea on any single one of these, run evol <command> -h for more information on a specific command. the way that every subcommand has its own little help moment… obsessed 😭

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and that's the whole page, we ate and left no crumbs 💖

this was ProDy version 2.4.1, dated February 2024 — love that for us, mwah 🎀