BEST: Bayesian estimation of species trees under the coalescent model

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 wit...

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Bibliographic Details
Published inBioinformatics Vol. 24; no. 21; pp. 2542 - 2543
Main Author Liu, Liang
Format Journal Article
LanguageEnglish
Published Oxford Oxford University Press 01.11.2008
Oxford Publishing Limited (England)
Subjects
Algorithms
Bayes Theorem
Biological and medical sciences
Computational Biology - methods
Fundamental and applied biological sciences. Psychology
General aspects
Markov Chains
Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects)
Models, Genetic
Monte Carlo Method
Phylogeny
Software
Tree
Models
Bioinformatics
Species
Estimation
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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@oeb.harvard.edu
Bibliography:ark:/67375/HXZ-1FP15WJQ-7
Associate Editor: Martin Bishop
istex:ADC20DF7837DC47C4F5E365563128850C118AD7D
ArticleID:btn484
ObjectType-Article-1
SourceType-Scholarly Journals-1
ObjectType-Feature-2
content type line 23
ISSN:1367-4803
1460-2059
1367-4811
DOI:10.1093/bioinformatics/btn484