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nf-core/muscle @ 0.0.0-0c7146d

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: 0.0.0-0c7146d
Total downloads: 1
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 0.0.0-0c7146d
Commit ID 135d883a43b1a2324b4112cd270cf22e20835533
Release Date 08 Apr 2026 18:58:04 (UTC)
Download URL https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fmuscle/0.0.0-0c7146d/download
OCI Store URL https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/muscle/blobs/sha256:7ab6ea33ef3cc814a7086bc20162bca79d861a845424c4b10b02b9cb7dc8020e
Size 3.3 KB
Checksum sha256:7ab6ea33ef3cc814a7086bc20162bca79d861a845424c4b10b02b9cb7dc8020e