Clustalw
From BioPerl
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.
References
- 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. pmid:7984417.
- 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. pmid:12824352.
- 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. pmid:9810230.
- Higgins DG, Bleasby AJ, and Fuchs R. CLUSTAL V: improved software for multiple sequence alignment. Comput Appl Biosci 1992 Apr; 8(2) 189-91. pmid:1591615.
- Higgins DG and Sharp PM. CLUSTAL: a package for performing multiple sequence alignment on a microcomputer. Gene 1988 Dec 15; 73(1) 237-44. pmid:3243435.
