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Book Sections Year : 2020

PhyloBayes: Bayesian Phylogenetics Using Site-heterogeneous Models

Abstract

PhyloBayes is a software program for Bayesian phylogenetic reconstruction. Compared to other programs, its main distinguishing feature is the implementation of the CAT model, which accounts for fine-grained variation across sites in amino acid preferences using a Bayesian non-parametric approach. This chapter provides a detailed step-by-step practical introduction to phylogenetic analyses using PhyloBayes, using as an example a previously published dataset addressing the phylogenetic position of Microsporidia within eukaryotes. Through this historically emblematic case of a long-branch attraction artifact, a complete analysis under site-homogeneous and site-heterogeneous models is conducted and interpreted, thus providing an illustration of why modeling pattern variation is so fundamental for reconstructing deep phylogenies.
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hal-02535342 , version 1 (10-04-2020)

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Attribution - NonCommercial - NoDerivatives

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  • HAL Id : hal-02535342 , version 1

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Nicolas Lartillot. PhyloBayes: Bayesian Phylogenetics Using Site-heterogeneous Models. Scornavacca, Celine; Delsuc, Frédéric; Galtier, Nicolas. Phylogenetics in the Genomic Era, No commercial publisher | Authors open access book, pp.1.5:1--1.5:16, 2020. ⟨hal-02535342⟩
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