BEAST (Bayesian Evolutionary Analysis Sampling Trees) 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.
If you use this application in your research, the recommended citation is Drummond AJ, Suchard MA, Xie D & Rambaut A (2012) Bayesian phylogenetics with BEAUti and the BEAST 1.7 Molecular Biology And Evolution 29: 1969-1973
To use BEAST, please set your environment using environment modules.
module avail BEAST
To select a module, type
module load BEAST/[ver]
where [ver] is the version of choice.
Environment variables set:
- $PATH
- $LD_LIBRARY_PATH
- $BEAST_EXAMPLES
Once your environment has been set, get your XML input in place and type
beast myinput.xml
There is an example available:
cp $BEAST_EXAMPLES/Benchmarks/benchmark1.xml . beast benchmark1.xml
Create a swarm command file (beast.swarm) with a single line for each run, e.g.:
beast file1.xml beast file2.xml beast file3.xml beast file4.xml
The environment module can be loaded using --module. Submit this swarm of jobs with the command:
swarm -f beast.swarm --module BEAST
Create a script file (sbatch.sh) like this:
#!/bin/bash #SBATCH --job-name beast module load beast beast myinput.xml
Then submit to the cluster like this:
sbatch sbatch.sh
Under some circumstances, GPUs can greatly accelerate computation. Include -beagle_GPU -beagle_order 2,1,0 with the beast commandline:
beast -beagle_GPU -beagle_order 2,1,0 myinput.xml
and be sure to allocate GPUs:
sbatch --constraint=gpuk20x --gres=gpu:k20x:2 sbatch.sh
Type beast -help at the prompt
