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nf-core/muscle @ 0.0.0-6c4ed3a

MUSCLE is a program for creating multiple alignments of amino acid or nucleotide sequences. A range of options are provided that give you the choice of optimizing accuracy, speed, or some compromise between the two

msa multiple sequence alignment phylogeny
Latest version: 0.0.0-6c4ed3a
Total downloads: 11
Source: nf-core/modules
Authors: @MGordon
Maintainers: @MGordon

Summary

MUSCLE is a program for creating multiple alignments of amino acid or nucleotide sequences. A range of options are provided that give you the choice of optimizing accuracy, speed, or some compromise between the two

Get started

Add the following snippet to your workflow script to include this module.

include { MUSCLE } from 'nf-core/muscle'

License

MIT License

Process
Name MUSCLE
Input 1 channel
#1 tuple
meta map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]
fasta file

Input sequences for alignment must be in FASTA format

 *.{fasta,fa,fna}
Output 9 channels
#1 log
*.log file

Log file of MUSCLE run

 *{.log}
#2 msf tuple
meta map

Groovy Map containing sample information
*.msf file

GCG Multiple Sequence File (MSF) alignment format (similar to CLUSTALW)

 *.{msf}
#3 html tuple
meta map

Groovy Map containing sample information
*.html file

Multiple sequence alignment produced in HTML format

 *.{html}
#4 phyi tuple
meta map

Groovy Map containing sample information
*.phyi file

Multiple sequence alignment produced in PHYLIP interleaved format

 *.{phyi}
#5 phys tuple
meta map

Groovy Map containing sample information
*.phys file

Multiple sequence alignment produced in PHYLIP sequential format

 *.{phys}
#6 tree tuple
meta map

Groovy Map containing sample information
*.tree file

NJ or UPGMA tree in Newick format produced from a multiple sequence alignment

 *.{tree}
#7 clustalw tuple
meta map

Groovy Map containing sample information
*.clw file

Multiple sequence alignment produced in ClustalW format without base/residue numbering

 *.{clw}
#8 versions
versions.yml file

File containing software versions

 versions.yml
#9 aligned_fasta tuple
meta map

Groovy Map containing sample information
*.afa file

Multiple sequence alignment produced in FASTA format

 *.{afa}
Tool Description Homepage
muscle MUSCLE is a multiple sequence alignment tool with high accuracy and throughput https://www.drive5.com/muscle
Version 0.0.0-6c4ed3a
Commit ID 6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date 23 Apr 2026 15:32:36 (UTC)
Download URL https://registry.nextflow.io/api/v1/modules/nf-core%2Fmuscle/0.0.0-6c4ed3a/download
OCI Store URL https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/muscle/blobs/sha256:8ef1ea5322263d84631ee3de9866d454c6cdd24cfa87fecfd73639f6d88490bd
Size 3.4 KB
Checksum sha256:8ef1ea5322263d84631ee3de9866d454c6cdd24cfa87fecfd73639f6d88490bd