BEAST

Description

BEAST 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, 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 add-ons. You can use the addonmanager-command to install the desired add-ons within your home-directory.

 $ module load beast
 $ 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=2000M

module load beast/2.4.0

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 a shorter variable where to find BEAST
BEAST_LIB="${EBROOTBEAST}/lib"

# use BEAST_EXTRA_LIBS variable to load BEAGLE and other 
# libraries from non-default locations
BEAST_EXTRA_LIBS="${BEAST_LIB}:${BEAGLE_LIB}"

# Add location of Beagle to LD_LIBRARY_PATH:
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