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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 its 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".

Simple Jobscript for BEAST

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

module load beast/2.6.3

beast input_beast.xml

Jobscript for BEAST with more Memory

high_memory_beast_job.sh
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#!/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/2.6.3

# 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 -cp ${BEAST_LIB}/launcher.jar beast.app.beastapp.BeastLauncher" # which program to execute

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

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

References