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Bioinformatics for DNA Sequence Analysis pp 113–137Cite as

Estimating Maximum Likelihood Phylogenies with PhyML

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 537))

Abstract

Our understanding of the origins, the functions and/or the structures of biological sequences strongly depends on our ability to decipher the mechanisms of molecular evolution. These complex processes can be described through the comparison of homologous sequences in a phylogenetic framework. Moreover, phylogenetic inference provides sound statistical tools to exhibit the main features of molecular evolution from the analysis of actual sequences. This chapter focuses on phylogenetic tree estimation under the maximum likelihood (ML) principle. Phylogenies inferred under this probabilistic criterion are usually reliable and important biological hypotheses can be tested through the comparison of different models. Estimating ML phylogenies is computationally demanding, and careful examination of the results is warranted. This chapter focuses on PhyML, a software that implements recent ML phylogenetic methods and algorithms. We illustrate the strengths and pitfalls of this program through the analysis of a real data set. PhyML v3.0 is available from http://atgc_montpellier.fr/phyml/.

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Acknowledgements

This work was supported by the “MITOSYS” grant from ANR. The chapter itself is the contribution 2007–08 of the Institut des Sciences de l'Evolution (UMR5554-CNRS).

Author information

Authors and Affiliations

  1. Laboratoire d’Informatique, de Robotique et de Microélectronique de Montpellier (LIRMM). Montpellier I I, UMR 5506-CNRS, Université, Montpellier, France

    Stéphane Guindon, Jean-François Dufayard & Olivier Gascuel

  2. Department of Statistics, University of Auckland, Auckland, New Zealand

    Stéphane Guindon

  3. Institut des Sciences de l’Evolution de Montpellier (ISEM), UMR 5554-CNRS, Université Montpellier I I, Montpellier, France

    Frédéric Delsuc

Authors
  1. Stéphane Guindon
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  2. Frédéric Delsuc
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  3. Jean-François Dufayard
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  4. Olivier Gascuel
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Editor information

Editors and Affiliations

  1. Dept. Bioquímica, Genética e Inmunología, Universidad de Vigo, Vigo, 36310, Spain

    David Posada

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© 2009 Humana Press, a part of Springer Science+Business Media, LLC

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Guindon, S., Delsuc, F., Dufayard, JF., Gascuel, O. (2009). Estimating Maximum Likelihood Phylogenies with PhyML. In: Posada, D. (eds) Bioinformatics for DNA Sequence Analysis. Methods in Molecular Biology, vol 537. Humana Press. https://doi.org/10.1007/978-1-59745-251-9_6

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  • DOI: https://doi.org/10.1007/978-1-59745-251-9_6

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  • Print ISBN: 978-1-58829-910-9

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