---
name: "muscle"
section: "1"
platform: "linux"
package: "muscle"
version: "1:5.1.0-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/muscle"
---

# muscle(1)

Multiple alignment program of protein sequences

## NAME

muscle - Multiple alignment program of protein sequences

## DESCRIPTION

MUSCLE is a multiple alignment program for protein sequences. MUSCLE stands for multiple sequence comparison by log-expectation. In the authors tests, MUSCLE achieved the highest scores of all tested programs on several alignment accuracy benchmarks, and is also one of the fastest programs out there.

## USAGE

### Align FASTA input, write aligned FASTA (AFA) output:

-

  muscle **-align** input.fa **-output** aln.afa

Align large input using Super5 algorithm if **-align** is too expensive, typically needed with more than a few hundred sequences:

-

  muscle **-super5** input.fa **-output** aln.afa

### Single replicate alignment:

-

  muscle **-align** input.fa **-perm** PERM **-perturb** SEED **-output** aln.afa muscle **-super5** input.fa **-perm** PERM **-perturb** SEED **-output** aln.afa

-

  PERM is guide tree permutation none, abc, acb, bca (default none). SEED is perturbation seed 0, 1, 2... (default 0 = don't perturb).

Ensemble of replicate alignments, output in Ensemble FASTA (EFA) format, EFA has one aligned FASTA for each replicate with header line "\<PERM.SEED":

-

  muscle **-align** input.fa **-stratified** **-output** stratified\_ensemble.efa muscle **-align** input.fa **-diversified** **-output** diversified\_ensemble.afa

**-replicates** N

-

  Number of replicates, defaults 4, 100, 100 for stratified,

-

  diversified, resampled. With **-stratified** there is one replicate per guide tree permutation, total is 4 x N.

Generate resampled ensemble from existing ensemble by sampling columns with replacement:

-

  muscle **-resample** ensemble.efa **-output** resampled.efa

**-maxgapfract** F

-

  Maximum fraction of gaps in a column (F=0..1, default 0.5).

**-minconf** CC

-

  Minimum column confidence (CC=0..1, default 0.5).

If ensemble output filename has @, then one FASTA file is generated for each replicate where @ is replaced by perm.s, otherwise all replicates are written to one EFA file.

### Calculate disperson of an ensemble:

-

  muscle **-disperse** ensemble.efa

### Extract replicate with highest total CC (diversified input recommended):

-

  muscle **-maxcc** ensemble.efa **-output** maxcc.afa

### Extract aligned FASTA files from EFA file:

-

  muscle **-efa\_explode** ensemble.efa

### Convert FASTA to EFA, input has one filename per line:

-

  muscle **-fa2efa** filenames.txt **-output** ensemble.efa

Update ensemble by adding two sequences of digits to each replicate, digits are column confidence (CC) values, e.g. "73" means CC=0.73, "++" is CC=1.0:

-

  muscle **-addconfseqs** ensemble.efa **-output** ensemble\_cc.efa

Calculate letter confidence (LC) values, **-ref** specifies the alignment to compare against the ensemble (e.g. from **-maxcc**), output is in aligned FASTA format with LC values 0, 1 ... 9 instead of letters:

-

  muscle **-letterconf** ensemble.efa **-ref** aln.afa **-output** letterconf.afa

**-html** aln.html

-

  Alignment colored by LC in HTML format.

**-jalview** aln.features

-

  Jalview feature file with LC values and colors.

### More documentation at:

-

  https://drive5.com/muscle

## AUTHOR

 This manpage was written by Andreas Tille for the Debian distribution and\
  can be used for any other usage of the program.