BEST: Bayesian estimation of species trees under the coalescent model

被引：286

作者：

Liu, Liang ^{[1
]}

机构：

[1] Harvard Univ, Museum Comparat Zool, Cambridge, MA 02138 USA

来源：

BIOINFORMATICS | 2008年 / 24卷 / 21期

基金：

美国国家科学基金会;

关键词：

D O I：

10.1093/bioinformatics/btn484

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

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.

引用

页码：2542 / 2543

页数：2

共 14 条

[1]

[Anonymous], 2004, Inferring Phylogenies

[2] High-resolution species trees without concatenation [J].

Edwards, Scott V. ;

Liu, Liang ;

Pearl, Dennis K. .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2007, 104 (14) :5936-5941

[3]

HASTINGS WK, 1970, BIOMETRIKA, V57, P97, DOI 10.1093/biomet/57.1.97

[4] MRBAYES: Bayesian inference of phylogenetic trees [J].

Huelsenbeck, JP ;

Ronquist, F .

BIOINFORMATICS, 2001, 17 (08) :754-755

[5] OPTIMIZATION BY SIMULATED ANNEALING [J].

KIRKPATRICK, S ;

GELATT, CD ;

VECCHI, MP .

SCIENCE, 1983, 220 (4598) :671-680

[6]

Liti G, 2006, GENETICS, V174, P839, DOI 10.1534/genetics.106.062166

[7]

LIU L, 2006, THESIS OHIO STATE U, P46

[8] Estimating species trees using multiple-allele DNA sequence data [J].

Liu, Liang ;

Pearl, Dennis K. ;

Brumfield, Robb T. ;

Edwards, Scott V. .

EVOLUTION, 2008, 62 (08) :2080-2091

[9] Species trees from gene trees: Reconstructing Bayesian posterior distributions of a species phylogeny using estimated gene tree distributions [J].

Liu, Liang ;

Pearl, Dennis K. .

SYSTEMATIC BIOLOGY, 2007, 56 (03) :504-514

[10] Inferring phylogeny despite incomplete lineage sorting [J].

Maddison, WP ;

Knowles, LL .

SYSTEMATIC BIOLOGY, 2006, 55 (01) :21-30

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