Awesome
BEAST X
BEAST X 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 X 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.
Download BEAST X
Download BEAST v10.5 binaries for Mac, Windows and UNIX/Linux
The previous major release of BEAST was v1.8.4 --- binaries for Mac, Windows and UNIX/Linux 
Other Downloads
Documentation
Development software
We use IntelliJ IDEA and java profiling via JProfile and YourKit
Acknowledgements
- This work was supported in part by the European Union Seventh Framework Programme for research, technological development and demonstration under Grant Agreement no. 278433-PREDEMICS and no. 725422-ReservoirDOCS, the Wellcome Trust through collaborator award 206298/Z/17/Z, NSF grant DMS 1264153 and NIH grants R01 HG006139, R01 AI107034, U19 AI135995 and R01 AI153044.