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Contents 1 BEAST 2 IS UNDER DEVELOPMENT 2 What is BEAST? 3 BEAST 2 Downloads 3.1 BEAST v2.0.c has been released 3.2 Version History 3.3 README 3.4 JAVADOC 4 BEAST 2 Tutorials 4.1 BEAST 2.0.x XML 4.2 Practicals 4.3 Error Messages 4.4 Beast2 Add-ons 4.5 FAQ 5 BEAST 2 Core 6 BEAST 2 Add-on

BEAST 2 IS UNDER DEVELOPMENT

Beast 2 is a complete rewrite of Beast 1, with the aim of eventually replacing it.

Curious and adventurous users can try it. Any feedback is appreciated.

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 features of BEAST 2 !

BEAST 2 Downloads

BEAST v2.0.c has been released

1st December 2011: What's new in this version?

• Mac OS X version: BEAST v2.0.c.dmg

• Windows version: BEAST v2.0.c.zip

• Linux/UNIX version: BEAST v2.0.c.tgz

Version History

README

JAVADOC

JavaDoc for plugin developers: http://beast2.cs.auckland.ac.nz/javadoc/index.html

BEAST 2 Tutorials

BEAST 2.0.x XML

Practicals

• Divergence Dating (Version 2.0)

• STAR BEAST

STARBEAST.pdf (BEAST 1.6.x)

Error Messages

Beast2 Add-ons

List of available Add-ons

FAQ

BEAST 2 Core

• http://code.google.com/p/beast2/

BEAST 2 Add-on

• Utilities http://code.google.com/p/beastii/

• BMA http://code.google.com/p/beastii/

• BDSSM http://code.google.com/p/beastii/

• Species trees from SNP and AFLP analysis http://code.google.com/p/snap-mcmc/