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Nucleic Acids Research, 2003, Vol. 31, No. 13 3497-3500
© 2003 Oxford University Press

Multiple sequence alignment with the Clustal series of programs

Ramu Chenna, Hideaki Sugawara1, Tadashi Koike1, Rodrigo Lopez2, Toby J. Gibson, Desmond G. Higgins3 and Julie D. Thompson*,4

European Molecular Biology Laboratory, Meyerhofstrasse 1, D-69117 Heidelberg, Germany 1 Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka-Ken 411-8540, Japan 2 European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK 3 Department of Biochemistry, University College Cork, Cork, Ireland 4 Laboratoire de Biologie et Génomique Structurales, Institut de Génétique et de Biologie Moléculaire et Cellulaire, (CNRS/INSERM/ULP), BP 10142, 67404 Illkirch Cedex, France

*To whom correspondence should be addressed. Tel: +33 388653200; Fax: +33 388653276; Email: julie{at}igbmc.u-strasbg.fr

The Clustal series of programs are widely used in molecular biology for the multiple alignment of both nucleic acid and protein sequences and for preparing phylogenetic trees. The popularity of the programs depends on a number of factors, including not only the accuracy of the results, but also the robustness, portability and user-friendliness of the programs. New features include NEXUS and FASTA format output, printing range numbers and faster tree calculation. Although, Clustal was originally developed to run on a local computer, numerous Web servers have been set up, notably at the EBI (European Bioinformatics Institute) (http://www.ebi.ac.uk/clustalw/).


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