For better experience, turn on JavaScript!



Tools for multiple protein sequence alignment. The algorithm uses a guide tree in alignment creation. There are two separate flavors of Clustal 2: Clustal W, the command-line version and Clustal X, the graphical version.




  • Operation: Multiple sequence alignment
  • Input: Protein sequence in FASTA format
  • Output: ClustalW with character counts; ClustalW; Pearson/FASTA; MSF; NEXUS; PHYLIP; SELEX; STOCKHOLM; VIENNA
  • Software interface: command-line interface; graphical 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: Science Foundation Ireland
  • Contact:
  • Collection: Clustal


Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG "Clustal W and Clustal X version 2.0."
PMID: 17846036

Higgins DG, Sharp PM "CLUSTAL: a package for performing multiple sequence alignment on a microcomputer" Gene, 73, 237-244
PMID: 3243435

Higgins DG, Thompson JD, Gibson TJ "Using CLUSTAL for multiple sequence alignments" Methods Enzymol., 266, 383-402
PMID: 8743695

Jeanmougin F, Thompson JD, Gouy M, Higgins DG, Gibson TJ "Multiple sequence alignment with Clustal X" Trends Biochem Sci., 23, 403-405
PMID: 9810230

Higgins,DG and Sharp,PM "Fast and sensitive multiple sequence alignments on a microcomputer" Comput. Appl. Biosci., 5, 151-153
PMID: 2720464

Higgins DG, Bleasby AJ, Fuchs R "CLUSTAL V: improved software for multiple sequence alignment" Comput. Appl. Biosci., 8, 189-191
PMID: 1591615

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

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

Chenna R, Sugawara H, Koike T, Lopez R, Gibson TJ, Higgins DG, Thompson JD "Multiple sequence alignment with the Clustal series of programs" Nucleic Acids Res., 31, 3497-3500
PMID: 12824352
PMCID: PMC168907

Download and documentation

If you find errors, please report here.