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Nucleic Acids Research Advance Access published online on May 25, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm333
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© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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The M-Coffee web server: a meta-method for computing multiple sequence alignments by combining alternative alignment methods

Sebastien Moretti1, Fabrice Armougom3, Iain M. Wallace2, Desmond G. Higgins2, Cornelius V. Jongeneel1 and Cedric Notredame3,*

1Swiss Institute of Bioinformatics, Bâtiment Génopode, UNIL, CH-101 Lausanne, 2Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland and 3Information Génomique et Structurale, CNRS UPR2589, Institute for Structural Biology and Microbiology (IBSM), Parc Scientifique de Luminy, 163 Avenue de Luminy, FR- 13288, Marseille cedex 09, France

*To whom correspondence should be addressed. Tel: +33 491 106 486; Fax: +33 491 106 489; Email: cedric.notredame{at}europe.com

Received January 31, 2007. Revised April 15, 2007. Accepted April 18, 2007.

The M-Coffee server is a web server that makes it possible to compute multiple sequence alignments (MSAs) by running several MSA methods and combining their output into one single model. This allows the user to simultaneously run all his methods of choice without having to arbitrarily choose one of them. The MSA is delivered along with a local estimation of its consistency with the individual MSAs it was derived from. The computation of the consensus multiple alignment is carried out using a special mode of the T-Coffee package [Notredame, Higgins and Heringa (T-Coffee: a novel method for fast and accurate multiple sequence alignment. J. Mol. Biol. 2000; 302: 205–217); Wallace, O'Sullivan, Higgins and Notredame (M-Coffee: combining multiple sequence alignment methods with T-Coffee. Nucleic Acids Res. 2006; 34: 1692–1699)] Given a set of sequences (DNA or proteins) in FASTA format, M-Coffee delivers a multiple alignment in the most common formats. M-Coffee is a freeware open source package distributed under a GPL license and it is available either as a standalone package or as a web service from www.tcoffee.org.


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