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

Detail

  • Operation: Multiple sequence alignment

  • Software interface: Command-line user interface

  • Language: C++

  • License: Public domain

  • Cost: Free

  • Version name: 5.1

  • Credit: -

  • Input: FASTA

  • Output: FASTA;CLUSTALW;HTML;PHYLIP;MSF

  • Contact: http://www.drive5.com/contact.html

  • Collection: -

  • Maturity: Mature

Publications

  • MUSCLE: multiple sequence alignment with high accuracy and high throughput.
  • Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. MUSCLE: multiple sequence alignment with high accuracy and high throughput. 2004; 32:1792-7. doi: 10.1093/nar/gkh340
  • https://doi.org/10.1093/nar/gkh340
  • PMID: 15034147
  • PMC: PMC390337
  • MUSCLE: a multiple sequence alignment method with reduced time and space complexity.
  • Edgar RC. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. 2004; 5:113. doi: 10.1186/1471-2105-5-113
  • https://doi.org/10.1186/1471-2105-5-113
  • PMID: 15318951
  • PMC: PMC517706

Download and documentation

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