Bayesian Evolutionary Analysis Sampling Trees is a cross-platform program for Bayesian analysis of molecular sequences using MCMC. The program is orientated toward (strict and relaxed) molecular clock analyses. It can be used as a method of constructing phylogenies, but it is also intended 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 uses an XML input format that allows the user to design and run a large range of models. We also include a program that can convert NEXUS files into this format.

The BEAST home page is at

Available modules

Packages with modules

Module NeSI Cluster
BEAST/2.4.7 pan
BEAST/1.8.2-goolf-1.5.14 pan
BEAST/1.8.4-gimkl-2017a-no-beagle pan
BEAST/2.2.1 pan
BEAST/2.4.3 pan


BEAST is released at no cost under the terms of the GNU Lesser General Public Licence.

Example scripts

Example script for the Pan cluster

#!/bin/bash -e

#SBATCH --job-name      MyBEASTJob
#SBATCH --account       nesi99999
#SBATCH --time          01:00:00
#SBATCH --cpus-per-task 16
#SBATCH --mem-per-cpu   4G
#SBATCH --output        MyBEASTJob.%j.out   # Include the job ID in the names
#SBATCH --error         MyBEASTJob.%j.err   # of the output and error files

module load BEAST/2.2.1

# Here Java is told it can use ( cpus-per-task * mem-per-cpu - 2GB ) = 62GB
export _JAVA_OPTS="-Xms62g -Xmx62g" 

srun beast -beagle -beagle_SSE -threads $SLURM_CPUS_PER_TASK input.xml


Please note the Java options in the above script. BEAST is a Java program, and Java will not automatically use all the memory which Slurm has allocated for it unless told to do so.

Long BEAST runs

If your Slurm job ends too early you can continue its calculation in a second job by way of the -resume option of BEAST2. For very long BEAST runs it may even make sense to deliberately break it into 1-week segments to get around our limits on maximum job duration.

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