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.

References:

• 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

• Type beast -help at the prompt
• BEAST wiki page
• BEAST2

• Module Name: BEAST (see the modules page for more information)
• Multithreaded/singlethreaded/MPI...
• environment variables set
  • PATH
  • LD_LIBRARY_PATH
  • BEAST_EXAMPLES
• Example files in $BEAST_EXAMPLES

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ mkdir /data/$USER/BEAST; cd /data/$USER/BEAST
[user@cn3144 BEAST]$ module load BEAST
[user@cn3144 BEAST]$ cp $BEAST_EXAMPLES/benchmark1.xml .
[user@cn3144 BEAST]$ beast benchmark1.xml

[user@cn3144 BEAST]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. BEAST.sh). For example:

#!/bin/bash
module load BEAST
beast -threads $SLURM_CPUS_PER_TASK myinput.xml

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] BEAST.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=gpuk80 --gres=gpu:k80:2 sbatch.sh

Create a swarmfile (e.g. BEAST.swarm). For example:

beast -threads $SLURM_CPUS_PER_TASK -prefix input1 input1.xml
beast -threads $SLURM_CPUS_PER_TASK -prefix input2 input2.xml
beast -threads $SLURM_CPUS_PER_TASK -prefix input3 input3.xml
beast -threads $SLURM_CPUS_PER_TASK -prefix input4 input4.xml

Submit this job using the swarm command.

swarm -f BEAST.swarm [-g #] [-t #] --module BEAST