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There are two versions of Clustal 2 multiple sequence alignment software: 1) Clustal W command-line tool and 2) Clustal X with graphical user interface.


Phylogeny; Sequence analysis; Nucleic acid sites, features and motifs; Nucleic acid structure analysis; Sequence sites, features and motifs


  • Operation: Multiple sequence alignment
  • Input: FASTA
  • Output: ClustalW with character counts; ClustalW; Pearson/FASTA; MSF; NEXUS; PHYLIP; SELEX; STOCKHOLM; VIENNA
  • Software interface: Command-line user interface
  • Language: C
  • Operating system: Linux; Mac OS X; Microsoft Windows
  • License: GNU Lesser GPL
  • Cost: Free
  • Version name: 2.1
  • Maturity: Mature
  • Credit: -
  • Contact: clustalw _at_
  • Collection: Clustal


Thompson JD, Higgins DG, Gibson TJ "CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice." Nucleic Acids Res. 1994 Nov 11;22(22):4673-80.
PMID: 7984417
PMCID: PMC308517

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