UNIT 2.3 Multiple Sequence Alignment Using ClustalW and ClustalX

  1. Julie D. Thompson1,
  2. Toby. J. Gibson2,
  3. Des G. Higgins3

Published Online: 1 AUG 2002

DOI: 10.1002/0471250953.bi0203s00

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

How to Cite

Thompson, J. D., Gibson, T. J. and Higgins, D. G. 2002. Multiple Sequence Alignment Using ClustalW and ClustalX. Current Protocols in Bioinformatics. 00:2.3:2.3.1–2.3.22.

Author Information

  1. 1

    Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch Cedex, France

  2. 2

    European Molecular Biology Laboratory, Heidelberg, Germany

  3. 3

    University College, Cork, Ireland

Publication History

  1. Published Online: 1 AUG 2002
  2. Published Print: JAN 2003


The Clustal programs are widely used for carrying out automatic multiple alignment of nucleotide or amino acid sequences. The most familiar version is ClustalW, which uses a simple text menu system that is portable to more or less all computer systems. ClustalX features a graphical user interface and some powerful graphical utilities for aiding the interpretation of alignments and is the preferred version for interactive usage. Users may run Clustal remotely from several sites using the Web or the programs may be downloaded and run locally on PCs, Macintosh, or Unix computers. The protocols in this unit discuss how to use ClustalX and ClustalW to construct an alignment, and create profile alignments by merging existing alignments.