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Empirical Profile Mixture Models for Phylogenetic Reconstruction

Quang S. Le 1 Olivier Gascuel 2, * Nicolas Lartillot 2 
* Corresponding author
2 MAB - Méthodes et Algorithmes pour la Bioinformatique
LIRMM - Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier
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 ( They run under Linux and MaxOSX operating systems. CONTACT:
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Submitted on : Wednesday, September 24, 2008 - 9:02:05 AM
Last modification on : Friday, August 5, 2022 - 3:02:17 PM
Long-term archiving on: : Friday, June 4, 2010 - 11:44:23 AM


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  • HAL Id : lirmm-00324090, version 1



Quang S. Le, Olivier Gascuel, Nicolas Lartillot. Empirical Profile Mixture Models for Phylogenetic Reconstruction. Bioinformatics, Oxford University Press (OUP), 2008, 29, pp.2317-2323. ⟨lirmm-00324090⟩



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