Latest revision as of 10:03, 22 November 2022

Application Details

• Description: BEAST is a cross-platform program for Bayesian analysis of molecular sequences using MCMC.
• Version: 1.8.3
• Modules: beast/1.8.3
• Licence: Free, open-source

Usage Examples

BEAST 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.

It can make use of highly-parallel processors such as those in 3D graphics boards (referred to as Graphics Processing Units or GPUs) found in many PCs. In general using it (even if not using a GPU) will improve the performance of BEAST. However, installing it for BEAST to use is not a simple operation presently (but we hope to fix this shortly) and it is not necessarily going to benefit all data sets. In particular, for the use of a GPU (and currently only NVidia ones are supported) to be efficient, long partitions are required (perhaps >500 unique site patterns).

Interactive

While logged into a reserved high memory node (c230):

[username@c230 ~]$ module add beast/1.8.3
[username@c230 ~]$ module add libbeagle/2.1.2 
[username@c230 ~]$ module add java/jdk1.8.0_102
[username@c230 ~]$ beast Random_Cratopus_BEAST.xml

Non Interactive

Using a SLURM script to run an array based processing beast processing script across the compute nodes:

#!/bin/bash
#SBATCH -J Random_BEAST
#SBATCH -N 1
#SBATCH -o %A-%a.log
#SBATCH -e %A-%a.err
#SBATCH -p compute

module add beast/1.8.3
module add libbeagle/2.1.2 
module add java/jdk1.8.0_102


for i in ${SLURM_ARRAY_TASK_ID}
do
        cp Random_Cratopus_BEAST.xml Random_Cratopus_BEAST_${SLURM_ARRAY_TASK_ID}.xml
        sed -i -e "s/Random_Cratopus_BEAST/Random_Cratopus_BEAST_${SLURM_ARRAY_TASK_ID}/g" Random_Cratopus_BEAST_${SLURM_ARRAY_TASK_ID}.xml
done

beast "Random_Cratopus_BEAST_${SLURM_ARRAY_TASK_ID}".xml

• Then submitting this to SLURM.

[username@login01 ~]$ sbatch BeastDEMO.job
Submitted job 345663

Further Information

• http://beast.bio.ed.ac.uk/
• http://beast.bio.ed.ac.uk/Tutorial_6
• http://beast.bio.ed.ac.uk/Tutorial_8

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