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From BEAST Software
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What is BEAST?
BEAST is a cross-platform program for Bayesian MCMC analysis of molecular sequences. 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.
New! Philippe Lemey has written some tutorials for using the phylogeography models described in Lemey, Rambaut, Drummond & Suchard (2009) Comput Biol 5: e1000520
Downloads
BEAST v1.5.3 has been released
9th December 2009: What's new in this version?
Tracer v1.5 has been released
Downloadable Practicals with Data
A Rough Guide to BEAST 1.4
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 beast-users-subscribe@googlegroups.com or go to the mailing list site:
http://groups.google.com/group/beast-users
Getting started
These tutorials use the graphical applications of BEAST to perform analyses using the provided example files:
We now have a BEAST manual for download as a single PDF file:
Citing BEAST
The recommended citation for this program is:
- Drummond AJ, Rambaut A (2007) "BEAST: Bayesian evolutionary analysis by sampling trees." BMC Evolutionary Biology 7:214 full text
To cite the relaxed clock model in BEAST:
- Drummond AJ, Ho SYW, Phillips MJ & Rambaut A (2006) PLoS Biology 4, e88. full text
To cite the Bayesian Skyline model in BEAST:
- Drummond AJ, Rambaut A & Shapiro B and Pybus OG (2005) Mol Biol Evol 22, 1185-1192. full text
The original MCMC paper was:
- Drummond AJ, Nicholls GK, Rodrigo AG & Solomon W (2002) Genetics 161, 1307-1320. full text
Note that this program uses models and techniques from a range of other publications which should be cited if possible.
Contents of this website
- Programs distributed as part of the BEAST package:
- BEAST Bayesian Evolutionary Analysis Sampling Trees
- BEAUti A simple user interface for creating input files to run BEAST.
- LogCombiner A program to combine log and tree files from multiple runs of BEAST
- TreeAnnotator A program for summarizing the information in a sample of trees produced by BEAST
- Programs distributed seperately:
- Tracer A program for analysing results from Bayesian MCMC programs such as BEAST & MrBayes
- FigTree A program for viewing trees including summary information produced by TreeAnnotator
- Version History
- Tutorials
- Additional Documentation Various miscellaneous documentation pages
- Benchmarks A page for posting performance comparisons for various systems
- Example XML Files
- Error Messages
- XML format documentation
- FAQ
- Glossary of terms and acronyms
- Publications using BEAST
BEAST Developers
The complete source code for BEAST is now distributed under the GNU Lesser General Public License and the source code, bug tracking database and information for developers is now hosted by Google:
http://beast-mcmc.googlecode.com/
Phylogenetic Bayesian MCMC Trials
This is the beginnings of a site devoted to creating a set of comparisons between different programs that perform Bayesian MCMC phylogenetics. The aim is to identify where these programs overlaps in terms of the models they implement and to provide data sets that can be used to test these models. This will allow us to cross-validate programs using independent implementations of the same models and to compare the efficiency of different sampling strategies.
Phylogenetic Bayesian MCMC Trials
Alexei Drummond and Andrew Rambaut
Copyright © 2002-2007 All rights reserved.
