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)
• 1.7.2 (EL6), using beagle-lib (SSE) to speed up computation.

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

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

Template:Connect test05 Once connected run

module load beast
beauti

How To Run

• To use the beagle library use the '-beagle_SSE -beagle_instances X' command line switches where 'X' equals to the number of requested Beagle library instances.
• To limit the number of computing cores Beast uses to the number requested from the batch system use the '-threads N' where 'N' is the number of threads Beast will use for posterior computation.