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Bioinformatics Advance Access originally published online on August 21, 2008
Bioinformatics 2008 24(20):2317-2323; doi:10.1093/bioinformatics/btn445
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© The Author 2008. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Empirical profile mixture models for phylogenetic reconstruction

Le Si Quang , Olivier Gascuel and Nicolas Lartillot *

Méthodes et Algorithmes pour la Bioinformatique. LIRMM, CNRS-UM2, 141 rue Ada, 34392 Montpellier Cedex 5, France

*To whom correspondence should be addressed.


  Abstract

Motivation: Previous studies have shown that accounting for site-specific amino acid replacement patterns using mixtures of stationary probability profiles offers a promising approach for improving the robustness of phylogenetic reconstructions in the presence of saturation. However, such profile mixture models were introduced only in a Bayesian context, and are not yet available in a maximum likelihood (ML) framework. In addition, these mixture models only perform well on large alignments, from which they can reliably learn the shapes of profiles, and their associated weights.

Results: In this work, we introduce an expectation–maximization algorithm for estimating amino acid profile mixtures from alignment databases. We apply it, learning on the HSSP database, and observe that a set of 20 profiles is enough to provide a better statistical fit than currently available empirical matrices (WAG, JTT), in particular on saturated data.

Availability: We have implemented these models into two currently available Bayesian and ML phylogenetic reconstruction programs. The two implementations, PhyloBayes, and PhyML, are freely available on our web site (http://atgc.lirmm.fr/cat). They run under Linux and MaxOSX operating systems.

Contact: nicolas.lartillot{at}lirmm.fr

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Martin Bishop

Received on May 16, 2008; revised on July 22, 2008; accepted on August 18, 2008

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[Abstract] [Full Text] [PDF]


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