Difference between revisions of "BEAST"

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__NOTOC__
 
__NOTOC__
 
__NOEDITSECTION__
 
__NOEDITSECTION__
[[Category:Software]][[Category:Bioinformatics]][[Category:Phylogenetics]]
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[[Category:Software]][[Category:Biology]][[Category:Phylogenetics]]
 
{|<!--Main settings - REQUIRED-->
 
{|<!--Main settings - REQUIRED-->
 
|{{#vardefine:app|beast}}
 
|{{#vardefine:app|beast}}
|{{#vardefine:url|http://www.beast2.org/wiki/index.php/Main_Page}}
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|{{#vardefine:url|http://www.beast2.org}}
 
|{{#vardefine:exe|1}} <!--Present manual instructions for running the software -->
 
|{{#vardefine:exe|1}} <!--Present manual instructions for running the software -->
 
|{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF-->
 
|{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF-->
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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.
 
<!--Modules-->
 
<!--Modules-->
==Required Modules==
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==Environment Modules==
[[Modules|modules documentation]]
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Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
===Serial===
 
*{{#var:app}}
 
 
==System Variables==
 
==System Variables==
 
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
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Beast is also available for use through the friendly web interface of the [http://galaxy.rc.ufl.edu/root?tool_id=beast UFRC Galaxy instance]. It's located in the "Phylogenetics" section.
 
Beast is also available for use through the friendly web interface of the [http://galaxy.rc.ufl.edu/root?tool_id=beast UFRC Galaxy instance]. It's located in the "Phylogenetics" section.
  
==Interactive beauti use==
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==Interactive BEAUti use==
In short, you have to use a [[GUI Programs|SLURM GUI]] session and specify the module you want as the default beast module could be different from the one you'd like to run.
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See [https://beast.community/beauti https://beast.community/beauti] for general documentation on using BEAUti.
  
E.g.
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* Start an [https://ood.rc.ufl.edu OnDemand] session (console or desktop)
module load gui
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* Load the beast module in the terminal
gui start --module beast/2.6.0 -e beauti
 
  
 
See [[GUI Programs]] for reference.
 
See [[GUI Programs]] for reference.
 
Some versions of BEAST/BEAUTI may be available in [https://ood.rc.ufl.edu OnDemand].
 
 
 
<!--Additional-->
 
<!--Additional-->
 
{{#if: {{#var: exe}}|==Additional Information==
 
{{#if: {{#var: exe}}|==Additional Information==
 
* Use -beagle_GPU beast command-line argument to invoke BEAST with GPU acceleration when running in a [[GPU_Access|GPU Job]]
 
* Use -beagle_GPU beast command-line argument to invoke BEAST with GPU acceleration when running in a [[GPU_Access|GPU Job]]
* To use CPU acceleration 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.
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* To use CPU acceleration with 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. Then, the job resource request should be equal to <code>nodes=1:ppn=X</code> where X = N + 1.
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* 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  
 +
#SBATCH --ntasks=1
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#SBATCH --cpus-per-task=X
 +
where X = N + 1.
 
* General performance considerations - [http://www.beast2.org/beagle-beast-2-in-cluster/ http://www.beast2.org/beagle-beast-2-in-cluster/].
 
* General performance considerations - [http://www.beast2.org/beagle-beast-2-in-cluster/ http://www.beast2.org/beagle-beast-2-in-cluster/].
* Beast2 plugins are installed into your personal directory. This means that you need to start Beauti and install plugins manually.
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 +
==Installing BEAST2 plugins==
 +
* Start an OnDemand session (console or desktop)
 +
* Load the beast module in the terminal
 +
* Run beauti; use the File/Manage Packages menu to select the add-ons to (un)install.
 +
Note: Beast2 plugins are installed into your personal directory.
 
|}}
 
|}}
 
{{#if: {{#var: conf}}|==Configuration==
 
{{#if: {{#var: conf}}|==Configuration==

Latest revision as of 14:27, 27 June 2023

Description

beast website  

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.

Environment Modules

Run module spider beast to find out what environment modules are available for this application.

System Variables

  • HPC_BEAST_DIR - installation directory

Galaxy

Beast is also available for use through the friendly web interface of the UFRC Galaxy instance. It's located in the "Phylogenetics" section.

Interactive BEAUti use

See https://beast.community/beauti for general documentation on using BEAUti.

  • Start an OnDemand session (console or desktop)
  • Load the beast module in the terminal

See GUI Programs for reference.

Additional Information

  • Use -beagle_GPU beast command-line argument to invoke BEAST with GPU acceleration when running in a GPU Job
  • To use CPU acceleration with 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 to
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=X

where X = N + 1.

Installing BEAST2 plugins

  • Start an OnDemand session (console or desktop)
  • Load the beast module in the terminal
  • Run beauti; use the File/Manage Packages menu to select the add-ons to (un)install.

Note: Beast2 plugins are installed into your personal directory.