Beastx

Description

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 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 beastx to find out what environment modules are available for this application.

System Variables

HPC_BEASTX_DIR - installation directory
HPC_BEASTX_BIN - executable directory
HPC_BEASTX_DOC - documentation directory

Additional Information

Load the beastx module in the terminal
Type "beast -h" to view usage

Interactive BEAST X and BEAUti use

See https://beast.community/beast and https://beast.community/beauti for general documentation on using BEAST X and BEAUti, respectively.

Start an OnDemand session (console or desktop)
Load the beastx module in the terminal
Type "beast" or "beauti" to launch the application

See GUI Programs for reference.

Beagle Use

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

Citation

If you publish research that uses beastx you have to cite it as follows:

Suchard MA, Lemey P, Baele G, Ayres DL, Drummond AJ & Rambaut A (2018) Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10 Virus Evolution 4, vey016. https://doi.org/10.1093/ve/vey016