Bayesian Evolutionary Analysis by Sampling Trees (BEAST) is a software package that performs phylogenetic tree analysis with user specified molecular clock models using the widely popular Bayesian Markov chain Monte Carlo (MCMC) methods. BEAST has its origins in modeling pathogen evolution in near real time but is also popular for other phylogenetic applications. BEAST is a well documented and flexible tool for modeling phylogenetics. Using BEAST at CARC offers more power for rigorous computations.
BEAST uses .xml files which contain sequences and model parameters. Because BEAST is capable of incorporating a diverse range of meta data and specific time modeling parameters, the graphical user interface BEAUTi allows users to upload nexus files and create .xml files with ease. Make sure that the version of beast in the module you load matches the version of BEAUTi used to generate the .xml files.
Once a .xml file is generated, beast can be easily run on CARC. An example .pbs script is as follows:
#!/bin/bash
#PBS -q default
#PBS -N BEASTjob
#PBS -l nodes=1:ppn=8
#PBS -l walltime=24:00:00
#PBS -j oe
cd $PBS_O_WORKDIR
module load beast2-2.5.2-intel-19.0.4-hcnoysj
beast my_data.xml
The output should be a job log (joined with any potential error file), and a .tree file for your downstream analysis. For more assistance with BEAST at CARC please email [email protected].