What is BEAST?
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 v1.X (currently version
v1.8.4). For details about BEAST2, an independent project led by the University of Auckland, please look here.
Getting started with BEAST
These tutorials use the graphical applications of BEAST to perform analyses using the provided example files:
Tutorial 1: Using sequences sampled at different points in time to estimate rates Tutorial 2: Estimating the divergence time of a monophyletic group using a known mutation rate And more Tutorials available.
Some downloadable packages containing tutorial worksheets and associated data. These are used in workshops and classes.
The recommended citation for this program is:
Drummond AJ, Suchard MA, Xie D & Rambaut A (2012) Bayesian phylogenetics with BEAUti and the BEAST 1.7 Molecular Biology And Evolution 29, 1969-1973 full text See this page for a more detailed list of publications for citing individual models and components.
BEAST is descended from earlier work:
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.
It 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.
BEAST-Users mailing list
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@example.com or go to the mailing list site: