BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

被引：5488

作者：

Bouckaert, Remco ^{[1
]}

Heled, Joseph ^{[1
]}

Kuehnert, Denise ^{[1
,2
]}

Vaughan, Tim ^{[1
,3
]}

Wu, Chieh-Hsi ^{[1
]}

Xie, Dong ^{[1
]}

Suchard, Marc A. ^{[4
,5
,6
]}

Rambaut, Andrew ^{[7
]}

Drummond, Alexei J. ^{[1
,8
]}

机构：

[1] Univ Auckland, Computat Evolut Grp, Dept Comp Sci, Auckland 1, New Zealand

[2] ETH, Dept Environm Syst Sci, Zurich, Switzerland

[3] Massey Univ, Allan Wilson Ctr Mol Ecol & Evolut, Palmerston North, New Zealand

[4] Univ Calif Los Angeles, David Geffen Sch Med, Dept Biomath, Los Angeles, CA 90095 USA

[5] Univ Calif Los Angeles, David Geffen Sch Med, Dept Human Genet, Los Angeles, CA 90095 USA

[6] Univ Calif Los Angeles, Sch Publ Hlth, Dept Biostat, Los Angeles, CA 90024 USA

[7] Univ Edinburgh, Inst Evolutionary Biol, Edinburgh, Midlothian, Scotland

[8] Univ Auckland, Allan Wilson Ctr Mol Ecol & Evolut, Auckland 1, New Zealand

来源：

PLOS COMPUTATIONAL BIOLOGY | 2014年 / 10卷 / 04期

基金：

美国国家卫生研究院; 美国国家科学基金会;

关键词：

MAXIMUM-LIKELIHOOD-ESTIMATION; SPECIES TREES; INFERENCE; RATES; SUBSTITUTIONS; SKYLINE; DNA;

D O I：

10.1371/journal.pcbi.1003537

中图分类号：

Q5 [生物化学];

学科分类号：

070307 [化学生物学];

摘要：

We present a new open source, extensible and flexible software platform for Bayesian evolutionary analysis called BEAST 2. This software platform is a re-design of the popular BEAST 1 platform to correct structural deficiencies that became evident as the BEAST 1 software evolved. Key among those deficiencies was the lack of post-deployment extensibility. BEAST 2 now has a fully developed package management system that allows third party developers to write additional functionality that can be directly installed to the BEAST 2 analysis platform via a package manager without requiring a new software release of the platform. This package architecture is showcased with a number of recently published new models encompassing birth-death-sampling tree priors, phylodynamics and model averaging for substitution models and site partitioning. A second major improvement is the ability to read/write the entire state of the MCMC chain to/from disk allowing it to be easily shared between multiple instances of the BEAST software. This facilitates checkpointing and better support for multi-processor and high-end computing extensions. Finally, the functionality in new packages can be easily added to the user interface (BEAUti 2) by a simple XML template-based mechanism because BEAST 2 has been re-designed to provide greater integration between the analysis engine and the user interface so that, for example BEAST and BEAUti use exactly the same XML file format.

引用

页数：6

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