BEAST Software - Bayesian Evolutionary Analysis Sampling Trees

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 (currently version v1.8). For details about BEAST v2 please look here.

What can BEAST do?

Downloading BEAST

Software and Downloads

Descriptions of the BEAST software and its associated utilities.

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 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:

• 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.

• Downloadable Practicals with Data

Citing BEAST 

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.

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
• 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/

BEAST clusters

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