Difference between revisions of "BEAST"
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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. | 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. | ||
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Revision as of 02:46, 10 August 2012
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. We include a simple to use user-interface program for setting up standard analyses and a suit of programs for analysing the results.
Execution Environment and 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 N'command line switches where 'N' equals to the number of requested Beagle library instances. - To limit the number of computing cores Beast will use for posterior computation to the number requested from the batch system use the
'-threads N'where 'N' is the number of threads.