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, 29 (8), 1969-73

Bayesian Phylogenetics With BEAUti and the BEAST 1.7

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Bayesian Phylogenetics With BEAUti and the BEAST 1.7

Alexei J Drummond et al. Mol Biol Evol.

Abstract

Computational evolutionary biology, statistical phylogenetics and coalescent-based population genetics are becoming increasingly central to the analysis and understanding of molecular sequence data. We present the Bayesian Evolutionary Analysis by Sampling Trees (BEAST) software package version 1.7, which implements a family of Markov chain Monte Carlo (MCMC) algorithms for Bayesian phylogenetic inference, divergence time dating, coalescent analysis, phylogeography and related molecular evolutionary analyses. This package includes an enhanced graphical user interface program called Bayesian Evolutionary Analysis Utility (BEAUti) that enables access to advanced models for molecular sequence and phenotypic trait evolution that were previously available to developers only. The package also provides new tools for visualizing and summarizing multispecies coalescent and phylogeographic analyses. BEAUti and BEAST 1.7 are open source under the GNU lesser general public license and available at http://beast-mcmc.googlecode.com and http://beast.bio.ed.ac.uk.

Figures

F<sc>IG.</sc> 1
FIG. 1
BEAUti GUI for importing data and specifying the evolutionary model.
F<sc>IG.</sc> 2
FIG. 2
Simultaneous phylogenetic and phenotypic trait reconstruction of Darwin's finches. Plotted are the maximum clade credibility tree and posterior estimate of the trait correlation matrix. We annotate the tree with estimates of selected posterior clade support values and the one significant nucleotide substitution local clock (in red) and the branches scale in expected substitutions per site. We depict correlation coefficients through their bivariate ellipse sizes, where more highly correlated phenotypes return narrower ellipses.
F<sc>IG.</sc> 3
FIG. 3
(a) Representative gene tree of mitochondrial DNA fragment from 16 Darwin's finches of four species (Geospiza fortis, G. magnirostris, Camarhynchus parvulus, and Certhidea olivacea). Nodes that have posterior clade probabilities of greater than 0.5 are labeled with their posterior clade probability. (b) The two most probable species trees (solid line represents most probable species tree; dashed line is second most probable). (c) Gene tree embedded in a point estimate of the species tree, including divergence times and effective population sizes. The x axis is divergence time in units of substitutions per site and the y axis is proportional to effective population size.

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