MUSCLE(1)

💅 MUSCLE(1) — the Muscle Manual, bestie edition 🦋

okay so you're here because you wanna line up some protein sequences and you heard the muscle page is the place. welcome to the Muscle Manual, girlie. let's get into it 💖

✨ NAME ✨

muscle — Multiple Protein Sequence Alignment 🧬

✨ SYNOPSIS ✨

muscle -in input file (fasta) [-out output file (default fasta)]
       [-diags] [-log log file] [-maxiters n] [-maxhours n] [-maxmb m]
       [-html] [-msf] [-clw] [-clwstrict] [-log[a] logfile] [-quiet]
       [-stable] [-group] [-version]

✨ DESCRIPTION ✨

ok so real talk: this manual page is just a lil brief rundown of the muscle command. it's giving "overview", not "novel". 📖✨

what does it do tho? muscle aligns protein sequences, and it's considered superior and faster than Clustal W. no cap. 🔥

✨ OPTIONS ✨

here's the whole menu, bestie. every single one. i'm not skipping a thing, that's not the vibe. 💅

• -in input file — path to your FASTA formatted input file. this is the food your alignment eats. 🍓
• -out output file — path to the output file. FASTA formatted by default, because that's the default aesthetic. ✨
• -diags — find diagonals (faster for similar sequences). lowkey a shortcut when your sequences are already kinda twinning. 🦋
• -maxiters n — maximum number of iterations (integer, default 16). sixteen lil glow-up rounds, periodt. 🔁
• -maxhours n — maximum time to iterate in hours (default no limit). so by default it'll just keep going like it's got nowhere to be. 😭
• -maxmb m — maximum memory to allocate in Mb (default 80% of RAM). it's taking 80% of your RAM, that's just the arrangement. 💀
• -html — write output in HTML format (default FASTA). for when you want your alignment to be web. 🌈
• -msf — write output in MSF format (default FASTA). 🎀
• -clw — write output in Clustal W format (default FASTA). 🫶
• -clwstrict — as -clw, but with a ´CLUSTAL W (1.81)´ header. it's -clw but with a name tag, basically. iconic behavior. 👑
• -log[a] logfile — log to file (append if -loga, overwrite if -log). so -log says "fresh start", -loga says "keep the receipts". 📝
• -quiet — do not write progress messages to stderr. for the girlies who want silence and vibes only. 🤫
• -stable — output sequences in input order (default is -group). keeping everything exactly where it started. 🧚
• -group — group sequences by similarity (this is the default). so if you don't say anything, this is what happens. ⭐
• -version — display version information and exit. quick lil "who am i" then she's gone. 👋

✨ SEE ALSO ✨

go check out the cousins: clustalw(1), seaview(1), t_coffee(1). 🌸

✨ AUTHORS ✨

• Robert Elgar — wrote Muscle. the actual legend. 👑
• Steffen Moeller <moeller@debian.org> — wrote this manpage. 📝
• Charles Plessy <charles-debian-nospam@plessy.org> — updated this manpage. the glow-up maintainer. ✨

✨ COPYRIGHT ✨

Copyright © 2003, 2004 Steffen Moeller (manpage)
Copyright © 2007, 2008 Charles Plessy (manpage)

Muscle is in the public domain, and therefore not subjected to copyright. so like, it's free free. 🕊️

this manual page was written by Steffen Moeller moeller@debian.org for the Debian(TM) system (but may be used by others). permission is granted to copy, distribute and/or modify this document as if it were in public domain. so go wild, bestie, respectfully. 💜

⚠️ friendly reminder that this was a brief page, so if you need the deep lore, go read the actual Muscle docs. i'm just the messenger with good vibes. 🙈

okay that's the whole thing!! this page is muscle 3.7, dated 02/06/2008, and it lives in section 1 of the manual — <rainbow>MUSCLE(1)</rainbow>, mwah 💋 stay aligned, bestie 🫶✨