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_LIB - library directory
• HPC_BEAST_DOC - docs directory

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