Difference between revisions of "BEAST"

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__NOTOC__
 
__NOTOC__
 
__NOEDITSECTION__
 
__NOEDITSECTION__
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[[Category:Software]][[Category:Bioinformatics]]
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[[Category:Software]][[Category:Biology]][[Category:Phylogenetics]]
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<!-- ########  Template Configuration ######## -->
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{|<!--Main settings - REQUIRED-->
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<!--Edit definitions of the variables used in template calls
 
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Required variables:
 
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app - lowercase name of the application e.g. "amber"
 
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url - url of the software page (project, company product, etc) - e.g. "http://ambermd.org/"
 
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Optional variables:
 
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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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-->
 
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{|
 
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<!--Main settings - REQUIRED-->
 
 
|{{#vardefine:app|beast}}
 
|{{#vardefine:app|beast}}
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|{{#vardefine:url|http://beast.bio.ed.ac.uk/Main_Page}}
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|{{#vardefine:url|http://www.beast2.org}}
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<!--Compiler and MPI settings - OPTIONAL -->
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|{{#vardefine:exe|1}} <!--Present manual instructions for running the software -->
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|{{#vardefine:intel|}} <!-- E.g. "11.1" -->
 
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|{{#vardefine:mpi|}} <!-- E.g. "openmpi/1.3.4" -->
 
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<!--Choose sections to enable - OPTIONAL-->
 
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|{{#vardefine:mod|1}} <!--Present instructions for running the software with modules -->
 
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|{{#vardefine:exe|}} <!--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-->
 
|{{#vardefine:pbs|}} <!--Enable PBS script wiki page link-->
 
|{{#vardefine:pbs|}} <!--Enable PBS script wiki page link-->
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<!--Description-->
 
<!--Description-->
 
{{#if: {{#var: url}}|
 
{{#if: {{#var: url}}|
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{{App_Description|app={{#var:app}}|url={{#var:url}}}}|}}
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{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}
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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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<!--Location-->
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<!--Modules-->
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{{App_Location|app={{#var:app}}|{{#var:ver}}}}
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==Environment Modules==
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==Available versions==
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Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
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* 1.6.2
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==System Variables==
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* 1.7.0
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* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
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* 1.7.1 (default)
 
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<!-- -->
 
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{{#if: {{#var: mod}}|==Running the application using modules==
 
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{{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}}
 
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* HPC_BEAST_BIN - executable directory
 
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* HPC_BEAST_LIB - library directory
 
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* HPC_BEAST_DOC - docs directory
 
  
 
==Galaxy==
 
==Galaxy==
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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.
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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.
 +
 
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==Interactive BEAUti use==
 +
See [https://beast.community/beauti https://beast.community/beauti] for general documentation on using BEAUti.
  
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==Interactive beauti use==
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* Start an [https://ood.rc.ufl.edu OnDemand] session (console or desktop)
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To connect to a test node, for example biotest, where you can run the graphical beauti software to build an xml file for the BEAST use the following or a similar command on a linux or MacOS X system:
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* Load the beast module in the terminal
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ssh USER@biotest.ufhpc -o ForwardX11=yes -o ForwardX11Trusted=yes -o ProxyCommand='ssh USER@bio.hpc.ufl.edu exec nc biotest %p'
 
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or add the following to your ~/.ssh/config file:
 
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Host biotest
 
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    User USER
 
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    KeepAlive yes
 
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    ProxyCommand ssh USER@bio.hpc.ufl.edu exec nc biotest %p
 
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    ForwardX11 yes
 
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    ForwardX11Trusted yes
 
  
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where USER is your username. After editing ~/.ssh/config you can just run the following command to connect:
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See [[GUI Programs]] for reference.
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  ssh biotest
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<!--Additional-->
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{{#if: {{#var: exe}}|==Additional Information==
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* Use -beagle_GPU beast command-line argument to invoke BEAST with GPU acceleration when running in a [[GPU_Access|GPU Job]]
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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  
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  #SBATCH --ntasks=1
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#SBATCH --cpus-per-task=X
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where X = N + 1.
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* General performance considerations - [http://www.beast2.org/beagle-beast-2-in-cluster/ http://www.beast2.org/beagle-beast-2-in-cluster/].
  
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Once connected run
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==Installing BEAST2 plugins==
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module load beast
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* Start an OnDemand session (console or desktop)
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beauti
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* Load the beast module in the terminal
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{{#if: {{#var: exe}}|==How To Run==
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* Run beauti; use the File/Manage Packages menu to select the add-ons to (un)install.
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WRITE INSTRUCTIONS ON RUNNING THE ACTUAL BINARY|}}
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Note: Beast2 plugins are installed into your personal directory. 
 +
|}}
 
{{#if: {{#var: conf}}|==Configuration==
 
{{#if: {{#var: conf}}|==Configuration==
 
See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.|}}
 
See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.|}}
 
{{#if: {{#var: pbs}}|==PBS Script Examples==
 
{{#if: {{#var: pbs}}|==PBS Script Examples==
 
See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}}
 
See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}}
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{{#if: {{#var: policy}}|==Usage policy==
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{{#if: {{#var: policy}}|==Usage Policy==
 
WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)|}}
 
WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)|}}
 
{{#if: {{#var: testing}}|==Performance==
 
{{#if: {{#var: testing}}|==Performance==

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.




Retrieved from "https://help.rc.ufl.edu/mediawiki/index.php?title=BEAST&oldid=27996"