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ClustalW2 / ClustalW / ClustalX

ClustalW2, ClustallW, and ClustalX are general purpose, multiple sequence alignment tools. Multiple alignments of protein sequences can identify conserved sequence regions. This is useful in designing experiments to test and modify the function of specific proteins, in predicting the function and structure of proteins and in identifying new members of protein families. Clustal is a general purpose multiple sequence alignment program for DNA or proteins. ClustalW is the command line version and ClustalX is the graphical version of Clustal. The current version is ClustalW2. It produces biologically meaningful multiple sequence alignments of divergent sequences by calculating the best match for the selected sequences and lining them up so that the identities, similarities and differences can be seen. Evolutionary relationships can be seen via viewing Cladograms or Phylograms.

Technical Expertise Required: 
No programming
Cost: 
Free
Website for more information: 
Additional Information: 
  • http://www.ebi.ac.uk/Tools/clustalw2/index.html
  • Higgins D., Thompson J., Gibson T., Thompson J.D., Higgins D.G., Gibson T.J.(1994)
  • CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.
  • Higgins, D.G., Thompson, J.D. and Gibson, T.J. (1996) Using CLUSTAL for multiple sequence alignments. Methods Enzymol., 266:383-402. Nucleic Acids Research 22: 4673-4680.
  • Larkin M.A., Blackshields G., Brown N.P., Chenna R., McGettigan P.A., McWilliam H.*, Valentin F.*, Wallace I.M., Wilm A., Lopez R.*, Thompson J.D., Gibson T.J. and Higgins D.G. (2007),ClustalW and ClustalX version 2, Bioinformatics 2007 23(21): 2947-2948.
  • Using ClustalX for multiple sequence, Tuimala, J (tutorial available at http://www.clustal.org/)
Platform: 
Windows, Mac OS X, and Linux
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