BEAST: Difference between revisions

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.

@@ Line 1: / Line 1: @@
 __NOTOC__
 __NOEDITSECTION__
-[[Category:Software]][[Category:Bioinformatics]]
+[[Category:Software]][[Category:Biology]][[Category:Phylogenetics]]
-<!-- ########  Template Configuration ######## -->
+{|<!--Main settings - REQUIRED-->
-<!--Edit definitions of the variables used in template calls
-Required variables:
-app - lowercase name of the application e.g. "amber"
-url - url of the software page (project, company product, etc) - e.g. "http://ambermd.org/"
-Optional variables:
-INTEL - Version of the Intel Compiler e.g. "11.1"
-MPI - MPI Implementation and version e.g. "openmpi/1.3.4"
--->
-{|
-<!--Main settings - REQUIRED-->
 |{{#vardefine:app|beast}}
-|{{#vardefine:url|http://beast.bio.ed.ac.uk/Main_Page}}
+|{{#vardefine:url|http://www.beast2.org}}
-<!--Compiler and MPI settings - OPTIONAL -->
+|{{#vardefine:exe|1}} <!--Present manual instructions for running the software -->
-|{{#vardefine:intel|}} <!-- E.g. "11.1" -->
-|{{#vardefine:mpi|}} <!-- E.g. "openmpi/1.3.4" -->
-<!--Choose sections to enable - OPTIONAL-->
-|{{#vardefine:mod|1}} <!--Present instructions for running the software with modules -->
-|{{#vardefine:exe|}} <!--Present manual instructions for running the software -->
 |{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF-->
 |{{#vardefine:pbs|}} <!--Enable PBS script wiki page link-->
@@ Line 31: / Line 16: @@
 <!--Description-->
 {{#if: {{#var: url}}|
-{{App_Description|app={{#var:app}}|url={{#var:url}}}}|}}
+{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}
 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.
-<!--Location-->
+<!--Modules-->
-{{App_Location|app={{#var:app}}|{{#var:ver}}}}
+==Environment Modules==
-==Installed versions==
+Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
-* 1.6.2
+==System Variables==
-* 1.7.0
+* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
-* 1.7.1 (default)
-<!-- -->
+==Galaxy==
-{{#if: {{#var: mod}}|==Running the application using modules==
+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.
-{{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}}
-* HPC_BEAST_BIN - executable directory
+==Interactive BEAUti use==
-* HPC_BEAST_LIB - library directory
+See [https://beast.community/beauti https://beast.community/beauti] for general documentation on using BEAUti.
-* HPC_BEAST_DOC - docs directory
-==Interactive beauti use==
+* Start an [https://ood.rc.ufl.edu OnDemand] session (console or desktop)
-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:
+* Load the beast module in the terminal
- ssh USER@biotest.ufhpc -o ForwardX11=yes -o ForwardX11Trusted=yes -o ProxyCommand='ssh USER@bio.hpc.ufl.edu exec nc biotest %p'
-or add the following to your ~/.ssh/config file:
- Host biotest
-    User USER
-    KeepAlive yes
-    ProxyCommand ssh USER@bio.hpc.ufl.edu exec nc biotest %p
-    ForwardX11 yes
-    ForwardX11Trusted yes
-where USER is your username. After editing ~/.ssh/config you can just run the following command to connect:
+See [[GUI Programs]] for reference.
-  ssh biotest
+<!--Additional-->
+{{#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]]
+* 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
+  #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/].
-Once connected run
+==Installing BEAST2 plugins==
- module load beast
+* Start an OnDemand session (console or desktop)
- beauti
+* Load the beast module in the terminal
-{{#if: {{#var: exe}}|==How To Run==
+* Run beauti; use the File/Manage Packages menu to select the add-ons to (un)install.
-WRITE INSTRUCTIONS ON RUNNING THE ACTUAL BINARY|}}
+Note: Beast2 plugins are installed into your personal directory.
+|}}
 {{#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==
+{{#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==