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. It includes a simple to use user-interface program for setting up standard analyses and a suit of programs for analysing the results.

References:

• 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
• Bouckaert R., Vaughan T.G., Barido-Sottani J., Duchêne S., Fourment M., Gavryushkina A., et al. (2019) BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis. PLoS computational biology, 15(4), e1006650.

• Type beast -help at the prompt
• BEAST1
• BEAST2
• BEAST2 vs 1 Comparison

• Module Name: BEAST (see the modules page for more information)
• Multithreaded and GPU capable
• environment variables set
  • BEAST_LIB
  • 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 $BEAST_EXAMPLES/Benchmarks/benchmark1.xml .
[user@cn3144 BEAST]$ 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.

beast -beagle_GPU -beagle_CUDA -beagle_order 1,0 myinput.xml

and be sure to allocate GPUs:

sbatch --gres=gpu:p100:1 BEAST.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