View source for BEAST

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[[Category:Software]][[Category:Bioinformatics]][[Category:Phylogenetics]]
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INTEL - Version of the Intel Compiler e.g. "11.1"
MPI - MPI Implementation and version e.g. "openmpi/1.3.4"
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|{{#vardefine:app|beast}}
|{{#vardefine:url|http://beast.bio.ed.ac.uk/Main_Page}}
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<!--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.
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==Available versions==
* 1.6.2
* 1.7.0
* 1.7.1 (default)
* 1.7.2 (EL6), using beagle-lib (SSE) to speed up computation.
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{{#if: {{#var: mod}}|==Running the application using modules==
{{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}}
* 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 [http://galaxy.hpc.ufl.edu/root?tool_id=beast UF HPC Galaxy instance]. It's located in the "Phylogenetics" section.

==Interactive beauti use==
{{Connect_test05}}
Once connected run
 module load beast
 beauti
{{#if: {{#var: exe}}|==How To Run==
* 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.
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{{#if: {{#var: conf}}|==Configuration==
See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.|}}
{{#if: {{#var: pbs}}|==PBS Script Examples==
See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}}
{{#if: {{#var: policy}}|==Usage policy==
WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)|}}
{{#if: {{#var: testing}}|==Performance==
WRITE PERFORMANCE TESTING RESULTS HERE|}}
{{#if: {{#var: faq}}|==FAQ==
*'''Q:''' **'''A:'''|}}
{{#if: {{#var: citation}}|==Citation==
If you publish research that uses {{{app}}} you have to cite it as follows:
WRITE CITATION HERE
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