Description

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

Input

Name (Type)
Description
Pattern

fasta (file)

Input sequences for alignment must be in FASTA format

*.{fasta,fa,fna}

Output

Name (Type)
Description
Pattern

aligned_fasta (file)

Multiple sequence alignment produced in FASTA format

*.{afa}

msf (file)

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

*.{msf}

clustalw (file)

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

*.{clw}

phyi (file)

Multiple sequence alignment produced in PHYLIP interleaved format

*.{phyi}

phys (file)

Multiple sequence alignment produced in PHYLIP sequential format

*.{phys}

html (file)

Multiple sequence alignment produced in HTML format

*.{html}

tree (file)

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

*.{tree}

log (file)

Log file of MUSCLE run

*{.log}

versions (file)

File containing software versions

versions.yml
author
Github user MGordon
get in touch
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Tools

muscle
http://www.drive5.com/muscle/manual/license.html

MUSCLE is a multiple sequence alignment tool with high accuracy and throughput

drive5.com/muscle http://www.drive5.com/muscle/muscle.html#_Toc81224840 10.1093/nar/gkh340