W648 Nucleic Acids Research, 2007, Vol. 35, Web Server issue command line version of T-Coﬀee with the follow- ing syntax: t_coﬀee -other_pg seq_reformat -struc_in 5score_ascii4 -struc_in_f -action þkeep ‘[5-9]’ -in 5aln4 number_aln Where 5aln4 is the name of the alignment and 5score_ascii4 the name of the score_asccii ﬁle. This syntax will replace by a gap (‘-’) every residue having an ascii_score lower than 5 (green and blue residues on the colored output). CONCLUSION AND FUTURE DEVELOPMENTS M-Coﬀee provides biologists with a useful alternative to the a priori choice of an MSA method. Although M-Coﬀee does not entirely solve the question of which method should be used, its local scoring scheme makes it easier to read the alignment and determine which portions are the most informative. Further developments will include making more methods available, as well as making it possible to combine sequences and structures, using the Expresso protocol. ACKNOWLEDGEMENTS The development of the server was supported by CNRS (Centre National de la Recherche Scientiﬁque), by the Vital-IT frame work and by the European Union (ICGR- SIB FP6-026204). We thank Dr Pierre Pontarotti and Dr Vladimir Saudek for stimulating discussions. D.G.H. and I.M.W. are grateful to Science Foundation Ireland for funding. Funding to pay the Open Access publication charges for this article was provided by De´ partment des Science de la Vie, Centre National de la Recherche Scientiﬁque. Conﬂict of interest statement. None declared. REFERENCES 1. Notredame,C., Higgins,D.G. and Heringa,J. (2000) T-Coﬀee: A novel method for fast and accurate multiple sequence alignment. J. Mol. Biol., 302, 205–217. 2. Wallace,I.M., O’Sullivan,O., Higgins,D.G. and Notredame,C. (2006) M-Coﬀee: combining multiple sequence alignment methods with T-Coﬀee. Nucleic Acids Res., 34, 1692–1699. 3. Edgar,R.C. and Batzoglou,S. (2006) Multiple sequence alignment. Curr. Opin. Struct. 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