Difference between revisions of "BEAST"
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{{#if: {{#var: exe}}|==Additional Information== | {{#if: {{#var: exe}}|==Additional Information== | ||
* To use the beagle library use the <code>'-beagle_SSE -beagle_instances N'</code> command line switches where 'N' equals to the number of requested Beagle library instances. | * To use the beagle library use the <code>'-beagle_SSE -beagle_instances N'</code> 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 <code>'-threads N'</code> where 'N' is the number of threads. | + | * To limit the number of computing cores Beast will use for posterior computation to the number requested from the batch system use the <code>'-threads N'</code> where 'N' is the number of threads. Then, the job resource request should be equal to <code>nodes=1:ppn=X</code> where X = N + 1. |
|}} | |}} | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
Revision as of 13:28, 6 November 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.
Required Modules
Serial
- beast
System Variables
- HPC_{{#uppercase:beast}}_DIR - installation 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
Additional Information
- 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. Then, the job resource request should be equal tonodes=1:ppn=Xwhere X = N + 1.