BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis

被引:2665
作者
Bouckaert, Remco [1 ,2 ]
Vaughan, Timothy G. [3 ,4 ]
Barido-Sottani, Joelle [3 ,4 ]
Duchene, Sebastian [5 ]
Fourment, Mathieu [6 ]
Gavryushkina, Alexandra [7 ]
Heled, Joseph
Jones, Graham [8 ]
Kuehnert, Denise [2 ]
De Maio, Nicola [9 ]
Matschiner, Michael [10 ]
Mendes, Fabio K. [1 ]
Mueller, Nicola F. [3 ,4 ]
Ogilvie, Huw A. [11 ]
du Plessis, Louis [12 ]
Popinga, Alex [1 ]
Rambaut, Andrew [13 ]
Rasmussen, David [14 ]
Siveroni, Igor [15 ]
Suchard, Marc A. [16 ]
Wu, Chieh-Hsi [17 ]
Xie, Dong [1 ]
Zhang, Chi [18 ]
Stadler, Tanja [3 ,4 ]
Drummond, Alexei J. [1 ]
机构
[1] Univ Auckland, Ctr Computat Evolut, Auckland, New Zealand
[2] Max Planck Inst Sci Human Hist, Jena, Germany
[3] Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, CH-4058 Basel, Switzerland
[4] Swiss Inst Bioinformat, Lausanne, Switzerland
[5] Univ Melbourne, Dept Biochem & Mol Biol, Melbourne, Vic, Australia
[6] Univ Technol Sydney, Ithree Inst, Sydney, NSW, Australia
[7] Univ Otago, Dept Biochem, Dunedin 9016, New Zealand
[8] Univ Gothenburg, Dept Biol & Environm Sci, Box 461, SE-40530 Gothenburg, Sweden
[9] European Bioinformat Inst EMBL EBI, European Mol Biol Lab, Hinxton, Cambs, England
[10] Univ Basel, Dept Environm Sci, CH-4051 Basel, Switzerland
[11] Rice Univ, Dept Comp Sci, Houston, TX 77005 USA
[12] Univ Oxford, Dept Zool, Oxford OX1 3PS, England
[13] Univ Edinburgh, Ashworth Labs, Inst Evolutionary Biol, Edinburgh EH9 3FL, Midlothian, Scotland
[14] North Carolina State Univ, Dept Entomol & Plant Pathol, Raleigh, NC 27695 USA
[15] Imperial Coll London, Dept Infect Dis Epidemiol, Norfolk Pl, London W2 1PG, England
[16] Univ Calif Los Angeles, David Geffen Sch Med, Dept Biomath, Los Angeles, CA 90095 USA
[17] Univ Oxford, Dept Stat, Oxford OX1 3LB, England
[18] Chinese Acad Sci, Inst Vertebrate Paleontol & Paleoanthropol, Beijing, Peoples R China
基金
瑞士国家科学基金会; 欧洲研究理事会;
关键词
NUCLEOTIDE SUBSTITUTION; LIKELIHOOD-ESTIMATION; SPECIES TREES; GENE TREES; INFERENCE; MODELS; TIME; COALESCENT; SPECIATION; RADIATION;
D O I
10.1371/journal.pcbi.1006650
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
Elaboration of Bayesian phylogenetic inference methods has continued at pace in recent years with major new advances in nearly all aspects of the joint modelling of evolutionary data. It is increasingly appreciated that some evolutionary questions can only be adequately answered by combining evidence from multiple independent sources of data, including genome sequences, sampling dates, phenotypic data, radiocarbon dates, fossil occurrences, and biogeographic range information among others. Including all relevant data into a single joint model is very challenging both conceptually and computationally. Advanced computational software packages that allow robust development of compatible (sub-)models which can be composed into a full model hierarchy have played a key role in these developments. Developing such software frameworks is increasingly a major scientific activity in its own right, and comes with specific challenges, from practical software design, development and engineering challenges to statistical and conceptual modelling challenges. BEAST 2 is one such computational software platform, and was first announced over 4 years ago. Here we describe a series of major new developments in the BEAST 2 core platform and model hierarchy that have occurred since the first release of the software, culminating in the recent 2.5 release. Author summary Bayesian phylogenetic inference methods have undergone considerable development in recent years, and joint modelling of rich evolutionary data, including genomes, phenotypes and fossil occurrences is increasingly common. Advanced computational software packages that allow robust development of compatible (sub-)models which can be composed into a full model hierarchy have played a key role in these developments. Developing scientific software is increasingly crucial to advancement in many fields of biology. The challenges range from practical software development and engineering, distributed team coordination, conceptual development and statistical modelling, to validation and testing. BEAST 2 is one such computational software platform for phylogenetics, population genetics and phylodynamics, and was first announced over 4 years ago. Here we describe the full range of new tools and models available on the BEAST 2.5 platform, which expand joint evolutionary inference in many new directions, especially for joint inference over multiple data types, non-tree models and complex phylodynamics.
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页数:28
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