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ClustalW [1, 2] is one of the most commonly used tools for Multiple Sequence Alignment because it is fast and generally accurate enough for a general set of questions. Other tools such as MUSCLE, MAFFT, PROBCONS, T-Coffee provide more accuracy, sometimes with comparable speed. The software is available here as well as the graphical version, ClustalX [3].

Previous versions were called ClustalV [4] which itself was an upgrade of the Clustal package [5].

Alignment Format

The ClustalW multiple alignment format is a human and computer readable format that represents the alignment in ASCII text. Several other output options are available from the command line and interactive menu driven application.


  1. Thompson JD, Higgins DG, and 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. PubMed ID:7984417 | HubMed [clustalw]
  2. Chenna R, Sugawara H, Koike T, Lopez R, Gibson TJ, Higgins DG, and Thompson JD. Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res. 2003 Jul 1;31(13):3497-500. PubMed ID:12824352 | HubMed [NAR2003]
  3. Jeanmougin F, Thompson JD, Gouy M, Higgins DG, and Gibson TJ. Multiple sequence alignment with Clustal X. Trends Biochem Sci. 1998 Oct;23(10):403-5. PubMed ID:9810230 | HubMed [clustalx]
  4. Higgins DG, Bleasby AJ, and Fuchs R. CLUSTAL V: improved software for multiple sequence alignment. Comput Appl Biosci. 1992 Apr;8(2):189-91. PubMed ID:1591615 | HubMed [clustalv]
  5. Higgins DG and Sharp PM. CLUSTAL: a package for performing multiple sequence alignment on a microcomputer. Gene. 1988 Dec 15;73(1):237-44. PubMed ID:3243435 | HubMed [clustal]
All Medline abstracts: PubMed | HubMed
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