Difference between revisions of "BEAST"
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__NOTOC__ | __NOTOC__ | ||
__NOEDITSECTION__ | __NOEDITSECTION__ | ||
| − | [[Category:Software]][[Category: | + | [[Category:Software]][[Category:Biology]][[Category:Phylogenetics]] |
{|<!--Main settings - REQUIRED--> | {|<!--Main settings - REQUIRED--> | ||
|{{#vardefine:app|beast}} | |{{#vardefine:app|beast}} | ||
| − | |{{#vardefine:url|http://www.beast2.org | + | |{{#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--> | ||
| − | == | + | ==Environment Modules== |
| − | + | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | |
| − | |||
| − | |||
==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 | + | ==Interactive BEAUti use== |
| − | + | See [https://beast.community/beauti https://beast.community/beauti] for general documentation on using BEAUti. | |
| − | + | * Start an [https://ood.rc.ufl.edu OnDemand] session (console or desktop) | |
| − | + | * Load the beast module in the terminal | |
| − | |||
See [[GUI Programs]] for reference. | See [[GUI Programs]] for reference. | ||
| − | |||
| − | |||
| − | |||
<!--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. | + | * 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 | + | * 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 | ||
| + | #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. | + | |
| + | ==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 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.
- General performance considerations - http://www.beast2.org/beagle-beast-2-in-cluster/.
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.