From BEAST Software
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 & Nidia Trovao have written a downloadable tutorial on doing continuous diffusion phylogeography of rabies virus in racoons, Continuous_Phylogeography_1.7.5.zip described in Lemey P, Rambaut A, Welch JJ, Suchard MA. (2009) Mol Bio Evol, 27:1877-85
BEAST v1.7.5 has been released
14th February 2013: What's new in this version?
- BEAGLE is a high-performance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics package. It can make use of highly-parallel processors such as those in 3D graphics boards found in many PCs. This is an optional install but will improve BEAST performance in most cases. Instructions for installing and using BEAGLE with BEAST.
A Rough Guide to BEAST 1.4
- Manual for v1.4.x in PDF format - This manual primarily describes the input XML format to BEAST. Although it is now quite out of date it still provides the basis for more advanced BEAST use.
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:
These tutorials use the graphical applications of BEAST to perform analyses using the provided example files:
And more Tutorials available.
The recommended citation for this program is:
- Drummond AJ, Suchard MA, Xie D & Rambaut A "Bayesian phylogenetics with BEAUti and the BEAST 1.7" "Molecular Biology And Evolution" "in press" full text
The previous citation of BEAST is:
- Drummond AJ & Rambaut A (2007) "BEAST: Bayesian evolutionary analysis by sampling trees." BMC Evolutionary Biology 7, 214 full text
To cite the phylogeographic model in BEAST:
- Lemey P, Rambaut A, Drummond AJ & Suchard MA (2009) PLoS Computational Biology 5, e1000520. full text
To cite the continuous trait model in BEAST:
- Lemey P, Rambaut A, Welch JJ & Suchard MA (2010) Mol Biol Evol 27, 1877-1885. 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 random local clock model in BEAST:
- Drummond AJ & Suchard MA (2010) BMC Biology 8, 114. full text
To cite the Bayesian Skyline model in BEAST:
- Drummond AJ, Rambaut A, Shapiro B & Pybus OG (2005) Mol Biol Evol 22, 1185-1192. full text
To cite the Bayesian Skyride model in BEAST:
- Minin VN, Bloomquist EW & Suchard MA (2008) Mol Bio Evol 25, 1459-1471. full text
The original MCMC paper was:
- Drummond AJ, Nicholls GK, Rodrigo AG & Solomon W (2002) Genetics 161, 1307-1320. full text
Note that BEAST 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:
- Programs distributed seperately:
- Version History
- Additional Documentation Various miscellaneous documentation pages
- Benchmarks A page for posting performance comparisons for various systems
- Example XML Files
- Error Messages
- XML format documentation
- Glossary of terms and acronyms
- Publications using BEAST
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:
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.
These are the groups we know of providing public access to cluster resources that run BEAST. These groups are not associated with the BEAST developers and we can't provide assistance with using these resources.
- Computational Biology Service Unit http://cbsuapps.tc.cornell.edu/beast.aspx
Alexei Drummond, Andrew Rambaut and Marc Suchard
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