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Virus Evol. 2018 Jun 8;4(1):vey016. doi: 10.1093/ve/vey016. eCollection 2018 Jan.

Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10.

Author information

1
Department of Biomathematics, David Geffen School of MedicineUniversity of California, Los Angeles, 621 Charles E. Young Dr., South, Los Angeles, CA, 90095 USA.
2
Department of Biostatistics, Fielding School of Public HealthUniversity of California, Los Angeles, 650 Charles E, Young Dr., South, Los Angeles, CA, 90095 USA.
3
Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, 695 Charles E. Young Dr., South, Los Angeles, CA, 90095 USA.
4
Department of Microbiology and Immunology, Rega Institute, KU Leuven, Herestraat 49, 3000 Leuven, Belgium.
5
Center for Bioinformatics and Computational Biology, University of Maryland, College Park, 125 Biomolecular Science Bldg #296, College Park, MD 20742 USA.
6
Department of Computer Science, University of Auckland, 303/38 Princes St., Auckland, 1010 NZ.
7
Centre for Computational Evolution, University of Auckland, 303/38 Princes St., Auckland, 1010 NZ.
8
Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, Edinburgh, EH9 3FL UK.

Abstract

The Bayesian Evolutionary Analysis by Sampling Trees (BEAST) software package has become a primary tool for Bayesian phylogenetic and phylodynamic inference from genetic sequence data. BEAST unifies molecular phylogenetic reconstruction with complex discrete and continuous trait evolution, divergence-time dating, and coalescent demographic models in an efficient statistical inference engine using Markov chain Monte Carlo integration. A convenient, cross-platform, graphical user interface allows the flexible construction of complex evolutionary analyses.

KEYWORDS:

Bayesian inference; Markov chain Monte Carlo; phylodynamics; phylogenetics

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