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MUSCLE

MUSCLE

A program to create multiple sequence alignments of a large number of sequences. Prominent features are rapid sequence distance computation using k-mer counting, a profile function computing a log-expectation scores, and tree-dependent partitioning of the sequences.

Topic

Genomics; Sequencing; Sequence analysis

Details

  • Operation: Multiple sequence alignment
  • Input: FASTA
  • Output: FASTA; CLUSTALW; HTML; PHYLIP; MSF
  • Software interface: Command-line user interface
  • Language: C++
  • Operating system: Linux; Mac OS X; Microsoft Windows
  • License: Public domain
  • Cost: Free
  • Version name: 3.8.31
  • Maturity: Mature
  • Credit: -
  • Contact: http://www.drive5.com/contact.html
  • Collection: -

Publications

Edgar RC "MUSCLE: multiple sequence alignment with high accuracy and high throughput." Nucleic Acids Res. 2004 ;32(5) https://doi.org/10.1093/nar/gkh340
PMID: 15034147
PMCID: PMC390337


Edgar RC "MUSCLE: a multiple sequence alignment method with reduced time and space complexity." BMC Bioinformatics. 2004 Aug 19;5:113. https://doi.org/10.1186/1471-2105-5-113
PMID: 15318951
PMCID: PMC517706


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