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Bioinformatics Advance Access originally published online on September 17, 2008
Bioinformatics 2008 24(21):2542-2543; doi:10.1093/bioinformatics/btn484
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© The Author 2008. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

BEST: Bayesian estimation of species trees under the coalescent model

Liang Liu

Musuem of Comparative Zoology, Harvard University, Cambridge, MA, USA


  Abstract

Summary: BEST implements a Bayesian hierarchical model to jointly estimate gene trees and the species tree from multilocus sequences. It provides a new option for estimating species phylogenies within the popular Bayesian phylogenetic program MrBayes. The technique of simulated annealing is adopted along with Metropolis coupling as performed in MrBayes to improve the convergence rate of the Markov Chain Monte Carlo algorithm.

Availability: http://www.stat.osu.edu/~dkp/BEST.

Contact: lliu{at}oeb.harvard.edu

Associate Editor: Martin Bishop

Received on August 8, 2008; revised on September 9, 2008; accepted on September 9, 2008

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