---
name: "muscle3"
section: "1"
platform: "linux"
package: "muscle3"
version: "3.8.1551-3"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/muscle3"
---

# muscle3(1)

Multiple Protein Sequence Alignment

## 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

This manual page documents briefly the **muscle** command.

**muscle** aligns protein sequences and is considered superior and faster than Clustal W.

## OPTIONS

**-in** *input file*

Path to FASTA formatted input file

**-out** *output file*

Path to output file, FASTA formatted by default

- **-diags**

  Find diagonals (faster for similar sequences)

- **-maxiters** *n*

  Maximum number of iterations (integer, default 16)

- **-maxhours** *n*

  Maximum time to iterate in hours (default no limit)

- **-maxmb** *m*

  Maximum memory to allocate in Mb (default 80% of RAM)

- **-html**

  Write output in HTML format (default FASTA)

- **-msf**

  Write output in MSF format (default FASTA)

- **-clw**

  Write output in Clustal W format (default FASTA)

- **-clwstrict**

  As -clw, with ´CLUSTAL W (1.81)´ header

**-log\[a\]** *logfile*

Log to file (append if -loga, overwrite if -log)

- **-quiet**

  Do not write progress messages to stderr

- **-stable**

  Output sequences in input order (default is -group)

- **-group**

  Group sequences by similarity (this is the default)

- **-version**

  Display version information and exit

## SEE ALSO

[**clustalw**(1)](/clustalw/1.md), [**seaview**(1)](/seaview/1.md), [**t\_coffee**(1)](/t_coffee/1.md).

## AUTHORS

**Robert Elgar**

-

  Wrote Muscle.

**Steffen Moeller** \<moeller@debian.org\>

-

  Wrote this manpage.

**Charles Plessy** \<charles-debian-nospam@plessy.org\>

-

  Updated this manpage.

## 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.

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.