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A version of the Clustal 2 multiple sequence alignment program with a graphical interface.


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


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


Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG "The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools" Nucleic Acids Res., 25, 4876-4882
PMID: 9396791
PMCID: PMC147148

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