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.

Environment Modules

Run module spider beast to find out what environment modules are available for this application.

System Variables

• HPC_BEAST_DIR - installation 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

See https://beast.community/beauti for general documentation on using BEAUti.

• Start an OnDemand OnDemand session (console or desktop)
• Load the beast module in the terminal

See GUI Programs for reference.

Additional Information

• Use -beagle_GPU beast command-line argument to invoke BEAST with GPU acceleration when running in a GPU Job
• To use CPU acceleration 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

#SBATCH --ntasks=1
#SBATCH --cpus-per-task=X

where X = N + 1.

• General performance considerations - http://www.beast2.org/beagle-beast-2-in-cluster/.

Installing BEAST2 plugins

• Start an OnDemand session (console or desktop)
• Load the beast module in the terminal
• Run beauti; use the File/Manage Packages menu to select the add-ons to (un)install.

Note: Beast2 plugins are installed into your personal directory.