BEAST 2

Introduction

BEAST 2 is a cross-platform program for Bayesian phylogenetic analysis of molecular sequences.

For more information, please check its website: https://biocontainers.pro/tools/beast2 and its home page: https://www.beast2.org.

Versions

• 2.6.3

• 2.6.4

• 2.6.6

Commands

• applauncher

• beast

• beauti

• densitree

• loganalyser

• logcombiner

• packagemanager

• treeannotator

Module

You can load the modules by:

module load biocontainers
module load beast2

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run BEAST 2 on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 4
#SBATCH --job-name=beast2
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers beast2

beast -threads 4 -prefix input input.xml