BEAST 2 is a cross-platform program for Bayesian phylogenetic analysis of molecular sequences. It estimates rooted, time-measured phylogenies 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 2 uses Markov chain Monte Carlo (MCMC) to average over tree space, so that each tree is weighted proportional to its posterior probability. BEAST 2 includes a graphical user-interface for setting up standard analyses and a suit of programs for analysing the results.
The latest version of BEAST 2 is version 2.4.1:
Previous releases and version history
Previous releases and version history are available on the BEAST2 releases web page.
BEAST 2 is a rewrite of BEAST 1.x, placing a greater emphasis on modularity. This makes it easier to extend BEAST 2 via its package system. As a result, BEAST 2 has rapidly acquired the ability to perform a diverse array of model-based analyses. For a comparison of features/models currently available in BEAST 2 with those currently implemented in BEAST 1, refer to this features table.
As BEAST 2 is such a large and complicated application, first-time users may find coming to grips with the program and its capabilities a daunting task. We therefore encourage you to perform the following:
- Familiarise yourself with the terminology used by BEAST 2 users and developers.
- Work through the available tutorials, particularly those applicable to your data.
- Join the users mailing list by visiting the beast-users group or sending an email to firstname.lastname@example.org. This list is used to announce new versions and to advise users about bugs and other problems.
- Attend the Taming the BEAST workshop.
After completing these introductory steps, you’ll be well equipped to dive into the BEAST 2 Book.
BEAST 2 Packages
In BEAST 2, many models and analysis methods are implemented as BEAST 2 Packages. This means that the package is developed and maintained separately to BEAST 2 itself. To access these methods, you must download the corresponding packages in addition to BEAST 2. This is made easy by the BEAST 2 Package Manager, which is part of BEAST 2’s graphical user interface. See the Managing Packages page for details.
A list of known currently-available packages is provided in the BEAST 2/BEAST 1 comparison table.
Dealing with Problems and Performance Issues
While we aim to make using BEAST 2 a pleasant experience, problems do sometimes arise. In such cases, the following, please review the following information:
For performance-related issues, refer to this handy list of suggestions for improving performance.
BEAST 2 is designed to be extended. Prospective package developers should refer to the Package Development Guide.
Who develops BEAST?
BEAST 2 is developed by a team of scientists around the world. This web site is managed by the Computational Evolution Group.