Journal Article

Empirical profile mixture models for phylogenetic reconstruction

Le Si Quang, Olivier Gascuel and Nicolas Lartillot

in Bioinformatics

Volume 24, issue 20, pages 2317-2323
Published in print October 2008 | ISSN: 1367-4803
Published online August 2008 | e-ISSN: 1460-2059 | DOI:
Empirical profile mixture models for phylogenetic reconstruction

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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 ( They run under Linux and MaxOSX operating systems.


Supplementary information: Supplementary data are available at Bioinformatics online.

Journal Article.  6447 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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