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.
* Getting started (beast and beagle):
Options and more:
* Beast tests can be found here:
* bwHPC examples and a moab example script can be found here:
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.
BEAST 2: A Software Platform for Bayesian Evolutionary Analysis
Bouckaert, R., Heled, J., KÃ¼hnert, D., Vaughan, T., Wu, C-H., Xie,
D., Suchard, MA., Rambaut, A., & Drummond, A. J. (2014).
BEAST 2: A Software Platform for Bayesian Evolutionary Analysis.
PLoS Computational Biology, 10(4), e1003537. doi:10.1371/journal.pcbi.1003537
INSUFFICIENT MEMORY ERROR MESSAGES
'insufficient memory for the Java Runtime Environment'
This version of Beast/Beagle is a patched one. To keep the Java-files
running on the bwUniCluster, all the wrappers located in the Beast bin-folder
had been modified.
In case of problems, please contact: bwhpc (at) uni-konstanz.de
This module is available for all users.