BEAST: Difference between revisions
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== Description == | == Description == <!--T:1--> | ||
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BEAST<ref name="homepage">BEAST2 Homepage: http://beast2.org/</ref> 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<ref name="homepage">BEAST2 Homepage: http://beast2.org/</ref> 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. | ||
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BEAST can use the beagle-lib<ref>Beagle-lib Homepage: https://github.com/beagle-dev/beagle-lib</ref>, which is a high-performance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics packages. | BEAST can use the beagle-lib<ref>Beagle-lib Homepage: https://github.com/beagle-dev/beagle-lib</ref>, which is a high-performance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics packages. | ||
== Usage == | == Usage == <!--T:4--> | ||
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Loading the BEAST module with: <code>module load beast</code>, will automatically load it's dependencies, namely the <code>beagle-lib</code> and <code>java</code> modules, and set the environment variable <code>EBROOTBEAST</code> to point to the directory where BEAST's program files are located. | Loading the BEAST module with: <code>module load beast</code>, will automatically load it's dependencies, namely the <code>beagle-lib</code> and <code>java</code> modules, and set the environment variable <code>EBROOTBEAST</code> to point to the directory where BEAST's program files are located. | ||
=== Managing BEAST Packages/Add-ons === | === Managing BEAST Packages/Add-ons === <!--T:6--> | ||
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BEAST has been installed without any add-ons. You can use the <code>addonmanager</code>-command to install the desired add-ons within your home-directory. | BEAST has been installed without any add-ons. You can use the <code>addonmanager</code>-command to install the desired add-ons within your home-directory. | ||
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For more information on how to manage BEAST packages please read | For more information on how to manage BEAST packages please read | ||
the section "Server machines" at: http://www.beast2.org/managing-packages/ | the section "Server machines" at: http://www.beast2.org/managing-packages/ | ||
=== Simple Jobscript for BEAST === | === Simple Jobscript for BEAST === <!--T:9--> | ||
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=== Jobscript for BEAST with more Memory === | === Jobscript for BEAST with more Memory === <!--T:10--> | ||
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== References == | == References == <!--T:11--> | ||
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Revision as of 14:10, 5 September 2018
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 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=4000M
# Increase Maximum memory here if necessary:
# "BEAST_MEM" needs to be 250M lower than "--mem="
BEAST_MEM="-Xmx3750M"
module load beast/2.4.0
# Define a shorter variable where to find BEAST
BEAST="$EBROOTBEAST"
# Build a long java command:
CMD="java -Xms256m $BEAST_MEM" # set memory
CMD="$CMD -Djava.library.path=$BEAST/lib" # point to BEAST library
CMD="$CMD -jar $BEAST/lib/beast.jar" # which program to execute
echo ".................................."
echo "The Java command is \"$CMD\""
echo ".................................."
# Run the command:
$CMD input_beast.xml
References
- ↑ BEAST2 Homepage: http://beast2.org/
- ↑ Beagle-lib Homepage: https://github.com/beagle-dev/beagle-lib