Documentation

Help

Please have a look at ClustalX's builtin help menu or if you are using ClustalW use clustalw[2] -help or /help (depending on your platform and version of Clustal). Online versions (which might be out of date) can be found here: ClustalW and ClustalX. There are a couple of references on how to use ClustalW/X on the net. A very nice tutorial which also covers advanced features like using secondary structures for profile alignment is "Using ClustalX for multiple sequence" by Jarno Tuimala (local mirror).

References

• 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.
  (2007). Clustal W and Clustal X version 2.0. Bioinformatics, 23, 2947-2948.
• Chenna R, Sugawara H, Koike T, Lopez R, Gibson TJ, Higgins DG, Thompson JD.
  (2003). Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res., 31, 3497-3500.
• Jeanmougin F, Thompson JD, Gouy M, Higgins DG, Gibson TJ.
  (1998). Multiple sequence alignment with Clustal X. Trends Biochem Sci., 23, 403-405.
• Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG.
  (1997). The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res., 25, 4876-4882.
• Higgins DG, Thompson JD, Gibson TJ.
  (1996). Using CLUSTAL for multiple sequence alignments. Methods Enzymol., 266, 383-402.
• Thompson JD, Higgins DG, Gibson TJ.
  (1994). CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673-4680.
• Higgins DG.
  (1994). CLUSTAL V: multiple alignment of DNA and protein sequences. Methods Mol Biol., 25, 307-318
• Higgins DG, Bleasby AJ, Fuchs R.
  (1992). CLUSTAL V: improved software for multiple sequence alignment. Comput. Appl. Biosci., 8, 189-191.
• Higgins,DG and Sharp,PM
  (1989). Fast and sensitive multiple sequence alignments on a microcomputer. Comput. Appl. Biosci., 5, 151-153.
• Higgins,D.G. and Sharp,P.M.
  (1988). CLUSTAL: a package for performing multiple sequence alignment on a microcomputer. Gene, 73, 237-244.