BEAST: Bayesian Evolutionary Analysis by Sampling Trees

Overview

Journal BMC Evol Biol

Publisher Biomed Central

Specialty Biology

Date 2007 Nov 13

PMID 17996036

Citations 4351

Authors

Alexei J Drummond

Andrew Rambaut

Affiliations

Soon will be listed here.

Abstract

Background: The evolutionary analysis of molecular sequence variation is a statistical enterprise. This is reflected in the increased use of probabilistic models for phylogenetic inference, multiple sequence alignment, and molecular population genetics. Here we present BEAST: a fast, flexible software architecture for Bayesian analysis of molecular sequences related by an evolutionary tree. A large number of popular stochastic models of sequence evolution are provided and tree-based models suitable for both within- and between-species sequence data are implemented.

Results: BEAST version 1.4.6 consists of 81000 lines of Java source code, 779 classes and 81 packages. It provides models for DNA and protein sequence evolution, highly parametric coalescent analysis, relaxed clock phylogenetics, non-contemporaneous sequence data, statistical alignment and a wide range of options for prior distributions. BEAST source code is object-oriented, modular in design and freely available at http://beast-mcmc.googlecode.com/ under the GNU LGPL license.

Conclusion: BEAST is a powerful and flexible evolutionary analysis package for molecular sequence variation. It also provides a resource for the further development of new models and statistical methods of evolutionary analysis.

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References

Hasegawa M, Kishino H, Yano T . Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol. 1985; 22(2):160-74. DOI: 10.1007/BF02101694. View

Thorne J, Kishino H, Felsenstein J . An evolutionary model for maximum likelihood alignment of DNA sequences. J Mol Evol. 1991; 33(2):114-24. DOI: 10.1007/BF02193625. View

Gu X, Fu Y, Li W . Maximum likelihood estimation of the heterogeneity of substitution rate among nucleotide sites. Mol Biol Evol. 1995; 12(4):546-57. DOI: 10.1093/oxfordjournals.molbev.a040235. View

Huelsenbeck J, Ronquist F . MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics. 2001; 17(8):754-5. DOI: 10.1093/bioinformatics/17.8.754. View

Shapiro B, Drummond A, Rambaut A, Wilson M, Matheus P, Sher A . Rise and fall of the Beringian steppe bison. Science. 2004; 306(5701):1561-5. DOI: 10.1126/science.1101074. View

Waddell P, Steel M . General time-reversible distances with unequal rates across sites: mixing gamma and inverse Gaussian distributions with invariant sites. Mol Phylogenet Evol. 1998; 8(3):398-414. DOI: 10.1006/mpev.1997.0452. View

Lanave C, Preparata G, Saccone C, Serio G . A new method for calculating evolutionary substitution rates. J Mol Evol. 1984; 20(1):86-93. DOI: 10.1007/BF02101990. View

Suchard M, Redelings B . BAli-Phy: simultaneous Bayesian inference of alignment and phylogeny. Bioinformatics. 2006; 22(16):2047-8. DOI: 10.1093/bioinformatics/btl175. View

Drummond A, Rambaut A, Shapiro B, Pybus O . Bayesian coalescent inference of past population dynamics from molecular sequences. Mol Biol Evol. 2005; 22(5):1185-92. DOI: 10.1093/molbev/msi103. View

10.

Sanderson M . Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach. Mol Biol Evol. 2001; 19(1):101-9. DOI: 10.1093/oxfordjournals.molbev.a003974. View

11.

Uzzell T, Corbin K . Fitting discrete probability distributions to evolutionary events. Science. 1971; 172(3988):1089-96. DOI: 10.1126/science.172.3988.1089. View

12.

Kuhner M . LAMARC 2.0: maximum likelihood and Bayesian estimation of population parameters. Bioinformatics. 2006; 22(6):768-70. DOI: 10.1093/bioinformatics/btk051. View

13.

Goldman N, Yang Z . A codon-based model of nucleotide substitution for protein-coding DNA sequences. Mol Biol Evol. 1994; 11(5):725-36. DOI: 10.1093/oxfordjournals.molbev.a040153. View

14.

Huelsenbeck J, Rannala B . Frequentist properties of Bayesian posterior probabilities of phylogenetic trees under simple and complex substitution models. Syst Biol. 2005; 53(6):904-13. DOI: 10.1080/10635150490522629. View

15.

Wilson A, Sarich V . A molecular time scale for human evolution. Proc Natl Acad Sci U S A. 1969; 63(4):1088-93. PMC: 223432. DOI: 10.1073/pnas.63.4.1088. View

16.

Yoder A, Yang Z . Estimation of primate speciation dates using local molecular clocks. Mol Biol Evol. 2000; 17(7):1081-90. DOI: 10.1093/oxfordjournals.molbev.a026389. View

17.

Shapiro B, Rambaut A, Drummond A . Choosing appropriate substitution models for the phylogenetic analysis of protein-coding sequences. Mol Biol Evol. 2005; 23(1):7-9. DOI: 10.1093/molbev/msj021. View

18.

Beaumont M . Detecting population expansion and decline using microsatellites. Genetics. 1999; 153(4):2013-29. PMC: 1460853. DOI: 10.1093/genetics/153.4.2013. View

19.

Drummond A, Ho S, Phillips M, Rambaut A . Relaxed phylogenetics and dating with confidence. PLoS Biol. 2006; 4(5):e88. PMC: 1395354. DOI: 10.1371/journal.pbio.0040088. View

20.

Lunter G, Miklos I, Drummond A, Jensen J, Hein J . Bayesian coestimation of phylogeny and sequence alignment. BMC Bioinformatics. 2005; 6:83. PMC: 1087833. DOI: 10.1186/1471-2105-6-83. View