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BEAST Software - Bayesian Evolutionary Analysis Sampling Trees |
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BEAST is a cross-platform program for Bayesian analysis of molecular sequences using MCMC. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability. We include a simple to use user-interface program for setting up standard analyses and a suit of programs for analysing the results.
This website is for BEAST X v10.X (currently version v{{ site.beast_version }}). For details about BEAST2, an independent project led by the University of Auckland, please look here.
As an introduction to using BEAST we provide some basic introductory tutorials using the graphical applications of BEAST to perform analyses using provided example files.
The recommended citation for this program is: : Suchard MA, Lemey P, Baele G, Ayres DL, Drummond AJ & Rambaut A (2018) Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10 Virus Evolution 4, vey016. DOI:10.1093/ve/vey016
Drummond AJ, Nicholls GK, Rodrigo AG & Solomon W (2002) Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data. Genetics, 161, 1307-1320.
Rambaut A (2000) Estimating the rate of molecular evolution: incorporating non-contemporaneous sequences into maximum likelihood phylogenies. Bioinformatics, 16, 395-399.
Pybus OG & Rambaut A (2002) GENIE: estimating demographic history from molecular phylogenies. Bioinformatics, 18, 1404-1405.
BEAST is built on a large body of prior work and appropriate citations for individual modules, models and components will be listed when BEAST is run.
Users are strongly advised to join the BEAST mailing-list. This will be used to announce new versions and advise users about bugs and problems.
Send an email to [email protected] or go to the mailing list site:
http://groups.google.com/group/beast-users
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