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Numerical Optimization Techniques in Maximum Likelihood Tree Inference

Stéphane Guindon 1 Olivier Gascuel 2 
1 MAB - Méthodes et Algorithmes pour la Bioinformatique
LIRMM - Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier
Abstract : In this chapter, we present recent computational and algorithmic advances for improving the inference of phylogenetic trees from the analysis of homologous genetic sequences under the maximum likelihood criterion. In particular, we detail how the use of matrix algebra at the core of Felsenstein’s pruning algorithm, combined with the architecture of modern day computer processors, leads to efficient techniques for optimizing edge lengths. We also discuss some properties of the likelihood function when considering the optimization of the parameters of mixture models that are used to describe the variation of rates-across sites .
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Contributor : Olivier Gascuel Connect in order to contact the contributor
Submitted on : Wednesday, December 11, 2019 - 4:52:02 PM
Last modification on : Friday, August 5, 2022 - 3:02:17 PM




Stéphane Guindon, Olivier Gascuel. Numerical Optimization Techniques in Maximum Likelihood Tree Inference. Tandy Warnow. Bioinformatics and Phylogenetics: Seminal Contributions of Bernard Moret, 29, Springer, pp.21-38, 2019, Computational Biology (COBO), 978-3-030-10837-3. ⟨10.1007/978-3-030-10837-3_2⟩. ⟨pasteur-02405302⟩



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