M-Coffee: combining multiple sequence alignment methods with T-Coffee

TitleM-Coffee: combining multiple sequence alignment methods with T-Coffee
Publication TypeJournal Article
Year of Publication2006
AuthorsWallace IM, O'Sullivan O, Higgins DG, Notredame C
JournalNucleic Acids Res
Volume34
Pagination1692-9
Accession Number16556910
KeywordsAlgorithms, Reproducibility of Results, Sequence Alignment/ methods, Software
Abstract

We introduce M-Coffee, a meta-method for assembling multiple sequence alignments (MSA) by combining the output of several individual methods into one single MSA. M-Coffee is an extension of T-Coffee and uses consistency to estimate a consensus alignment. We show that the procedure is robust to variations in the choice of constituent methods and reasonably tolerant to duplicate MSAs. We also show that performances can be improved by carefully selecting the constituent methods. M-Coffee outperforms all the individual methods on three major reference datasets: HOMSTRAD, Prefab and Balibase. We also show that on a case-by-case basis, M-Coffee is twice as likely to deliver the best alignment than any individual method. Given a collection of pre-computed MSAs, M-Coffee has similar CPU requirements to the original T-Coffee. M-Coffee is a freeware open-source package available from http://www.tcoffee.org/.