BEAST

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Description

BEAST[1] 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.

BEAST can use the beagle-lib[2], which is a high-performance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics packages.

Usage

Loading the BEAST module with: module load beast, will automatically load it's dependencies, namely the beagle-lib and java modules, and set the environment variable EBROOTBEAST to point to the directory where BEAST's program files are located.

Managing BEAST Packages/Add-ons

BEAST has been installed without any packages (add-ons). You can use the packagemanager command (for BEAST v2.5.1 and newer; in older versions of BEAST, the command is addonmanager) to install the desired packages within your home directory.

 $ module load beast/2.5.1
 $ packagemanager -list
 Name    | Installation Status | Latest Version | Dependencies | Description
 --------------------------------------------------------------------------
 BEAST   | 2.5.1               | 2.5.0          |              | BEAST core
 --------------------------------------------------------------------------
 bacter  | NA                  | 2.2.0          |              | Bacterial ARG inference.
 BADTRIP | NA                  | 1.0.0          |              | Infer transmission time for [...]
 [...]
 SNAPP   | NA                  | 1.4.1          |              | SNP and AFLP Phylogenies
 [...]
   
 $ packagemanager -add SNAPP
 Package SNAPP is installed in ~/.beast/2.5/SNAPP.
 
 $ packagemanager -list
 Name    | Installation Status | Latest Version | Dependencies | Description
 --------------------------------------------------------------------------
 BEAST   | 2.5.1               | 2.5.0          |              | BEAST core
 --------------------------------------------------------------------------
 [...]
 SNAPP   | 1.4.1               | 1.4.1          |              | SNP and AFLP Phylogenies
 [...]
 $ module load beast/2.4.0
 $ addonmanager -list
 Name    | Installation Status | Latest Version | Dependencies | Description
 ---------------------------------------------------------------------------
 BEAST   | 2.4.0               | 2.4.8          |              | BEAST core
 ---------------------------------------------------------------------------
 bacter  | not installed       | 1.2.3          |              | Bacterial ARG inference.
 BASTA   | not installed       | 2.3.2          |              | Bayesian structured coalescent approximation
 [...]
 SNAPP   | not installed       | 1.3.0          |              | SNP and AFLP Phylogenies
 [...]
 
 $ addonmanager -add SNAPP
 Package SNAPP is installed in ~/.beast/2.4/SNAPP.
 
 $ addonmanager -list
 Name    | Installation Status | Latest Version | Dependencies | Description
 ---------------------------------------------------------------------------
 BEAST   | 2.4.0               | 2.4.8          |              | BEAST core
 ---------------------------------------------------------------------------
 [...]
 SNAPP   | 1.3.0               | 1.3.0          |              | SNP and AFLP Phylogenies
 [...]

For more information on how to manage BEAST packages please read the section "Server machines" at: http://www.beast2.org/managing-packages/

Simple Jobscript for BEAST

File : simple_beast_job.sh

#!/bin/bash
#SBATCH --account=def-someuser
#SBATCH --time=3:00:00
#SBATCH --mem-per-cpu=2000M

module load beast/2.5.1

beast input_beast.xml


Jobscript for BEAST with more Memory

File : high_memory_beast_job.sh

#!/bin/bash
#SBATCH --account=def-someuser
#SBATCH --time=3:00:00
#SBATCH --mem-per-cpu=4000M

# Increase Maximum memory here if necessary:
# "BEAST_MEM" needs to be 250M lower than "--mem="
BEAST_MEM="-Xmx3750M"

module load beast/2.5.1

# Define variables where to find BEAST and BEAGLE-lib
BEAST_LIB="${EBROOTBEAST}/lib"
BEAST_EXTRA_LIBS="${BEAST_LIB}:${BEAGLE_LIB}"
export LD_LIBRARY_PATH="${BEAGLE_LIB}:${LD_LIBRARY_PATH}"

# Build a long java command:
CMD="java -Xms256m ${BEAST_MEM}"                   # set memory
CMD="$CMD -Djava.library.path=${BEAST_EXTRA_LIBS}" # point to libraries
CMD="$CMD -jar ${BEAST_LIB}/beast.jar"             # which program to execute

echo ".................................."
echo "The Java command is \"${CMD}\""
echo ".................................."

# Run the command:
$CMD -beagle  input_beast.xml


References

  1. BEAST2 Homepage: http://beast2.org/
  2. Beagle-lib Homepage: https://github.com/beagle-dev/beagle-lib