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Bioinformatics Advance Access published online on August 21, 2008
Bioinformatics, 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 1, Olivier Gascuel 1 and Nicolas Lartillot 1,*

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

*To whom correspondence should be addressed. Dr. Nicolas Lartillot, E-mail: nicolas.lartillot{at}lirmm.fr


  Abstract

Motivation: Previous studies have shown that accounting for sitespecific 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 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 Maximum Likelihood 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

Associate Editor: Prof. Martin Bishop

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

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PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating
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[Abstract] [Full Text] [PDF]


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