BEAST

Description

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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. We include a simple to use user-interface program for setting up standard analyses and a suit of programs for analysing the results. Template:App Location

Available versions

• 1.6.2
• 1.7.0
• 1.7.1 (default)

Running the application using modules

To use beast with the environment modules system at HPC the following commands are available:

Get module information for beast:

$module spider beast

Load the default application module:

$module load beast

The modulefile for this software adds the directory with executable files to the shell execution PATH and sets the following environment variables:

• HPC_BEAST_DIR - directory where beast is located.
• HPC_BEAST_BIN - executable directory
• HPC_BEAST_DOC - docs directory
• BEAST - Beast directory
• _JAVA_OPTIONS - Default memory settings (-Xms=512m -Xmx1024m). They can be changed in the job script.

For example:

export _JAVA_OPTIONS="-Xms1024m -Xmx2048m"

Galaxy

Beast is also available for use through the friendly web interface of the UF HPC Galaxy instance. It's located in the "Phylogenetics" section.

Interactive beauti use

To connect to a test node, for example biotest, where you can run the graphical beauti software to build an xml file for the BEAST use the following or a similar command on a linux or MacOS X system:

ssh USER@biotest.ufhpc -o ForwardX11=yes -o ForwardX11Trusted=yes -o ProxyCommand='ssh USER@bio.hpc.ufl.edu exec nc biotest %p'

or add the following to your ~/.ssh/config file:

Host biotest
   User USER
   KeepAlive yes
   ProxyCommand ssh USER@bio.hpc.ufl.edu exec nc biotest %p
   ForwardX11 yes
   ForwardX11Trusted yes

where USER is your username. After editing ~/.ssh/config you can just run the following command to connect:

ssh biotest

Once connected run

module load beast
beauti