BEAST

Description

beast website  

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.

Required Modules

modules documentation

Serial

• beast

System Variables

• HPC_{{#uppercase:beast}}_DIR - installation directory
• HPC_BEAST_DOC - docs directory
• BEAST - Beast directory

Galaxy

Beast is also available for use through the friendly web interface of the UFRC Galaxy instance. It's located in the "Phylogenetics" section.

Interactive beauti use

Template:Connect test05 Once connected run

module load beast
beauti

Additional Information

• To use the beagle library use the '-beagle_SSE -beagle_instances N' command line switches where 'N' equals to the number of requested Beagle library instances.
• To limit the number of computing cores Beast will use for posterior computation to the number requested from the batch system use the '-threads N' where 'N' is the number of threads. Then, the job resource request should be equal to nodes=1:ppn=X where X = N + 1.
• General performance considerations - http://beast2.org/beagle-beast-2-in-cluster/.