Difference between revisions of "MrBayes"

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__NOTOC__
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[[Category:Phylogenetics]]
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{|<!--CONFIGURATION: REQUIRED-->
[[Category:Software]][[Category:Phylogenetics]]
 
<!-- ########  Template Configuration ######## -->
 
<!--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|mrbayes}}
 
|{{#vardefine:app|mrbayes}}
|{{#vardefine:url|http://mrbayes.sourceforge.net/}}
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|{{#vardefine:url|http://nbisweden.github.io/MrBayes}}
<!--Compiler and MPI settings - OPTIONAL -->
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<!--CONFIGURATION: OPTIONAL (|1}} means it's ON)-->
|{{#vardefine:intel|10.1}} <!-- E.g. "11.1" -->
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|{{#vardefine:conf|}}           <!--CONFIGURATION-->
|{{#vardefine:mpi|openmpi/1.2.7}} <!-- E.g. "openmpi/1.3.4" -->
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|{{#vardefine:exe|1}}           <!--ADDITIONAL INFO-->
<!--Choose sections to enable - OPTIONAL-->
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|{{#vardefine:job|}}           <!--JOB SCRIPTS-->
|{{#vardefine:mod|1}} <!--Present instructions for running the software with modules -->
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|{{#vardefine:policy|}}         <!--POLICY-->
|{{#vardefine:exe|}} <!--Present manual instructions for running the software -->
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|{{#vardefine:testing|}}       <!--PROFILING-->
|{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF-->
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|{{#vardefine:faq|}}             <!--FAQ-->
|{{#vardefine:pbs|1}} <!--Enable PBS script wiki page link-->
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|{{#vardefine:citation|}}       <!--CITATION-->
|{{#vardefine:policy|}} <!--Enable policy section -->
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|{{#vardefine:installation|}} <!--INSTALLATION-->
|{{#vardefine:testing|}} <!--Enable performance testing/profiling section -->
 
|{{#vardefine:faq|}} <!--Enable FAQ section -->
 
|{{#vardefine:citation|}} <!--Enable Reference/Citation section -->
 
 
|}
 
|}
<!-- ########  Template Body ######## -->
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<!--BODY-->
 
<!--Description-->
 
<!--Description-->
 
{{#if: {{#var: url}}|
 
{{#if: {{#var: url}}|
{{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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MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. MrBayes uses Markov chain Monte Carlo (MCMC) methods to estimate the posterior distribution of model parameters.
 
MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. MrBayes uses Markov chain Monte Carlo (MCMC) methods to estimate the posterior distribution of model parameters.
  
<!--Location-->
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<!--Modules-->
{{App_Location|app={{#var:app}}|{{#var:ver}}}}
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==Environment Modules==
<!--Versions-->
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Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
==Available versions==
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==System Variables==
* 3.1.2
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* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
<!-- -->
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<!--Configuration-->
==Running the application using modules==
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{{#if: {{#var: conf}}|==Configuration==
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See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.
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|}}
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<!--Run-->
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{{#if: {{#var: exe}}|==Additional Information==
  
Multiple versions of MrBayes are installed in /apps/mrbayes/3.1.2/, and can be used through loading different sets of module files.
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;For MPI jobs:
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* As a rule of thumb ntasks should be set to the total number of chains (MrBayes default is 4 chains * 2 runs = 8 chains)
  
For information about the MrBayes module options, run the module spider command:
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* As long as the number of cores is under 12, it is best to use a single node ("SBATCH --nodes=1") where nodes are physical computers as that will keep all communication within a single node.
$module spider mrbayes/3.1.2
 
  
'''All versions are compiled with Intel 10.1, so load this first in all cases.'''
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|}}
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<!--Job Scripts-->
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{{#if: {{#var: job}}|==Job Script Examples==
 +
See the [[{{PAGENAME}}_Job_Scripts]] page for {{#var: app}} Job script examples.
 +
|}}
 +
<!--Policy-->
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{{#if: {{#var: policy}}|==Usage Policy==
  
For the serial (single core) version load MrBayes:
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WRITE USAGE POLICY HERE (Licensing, usage, access).
$module load intel/10.1 mrbayes
 
  
The recommended MPI version is the OpenMPI 1.2.7 compiled version. To use this load:
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|}}
$module load intel/10.1 openmpi/1.2.7 mrbayes
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<!--Performance-->
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{{#if: {{#var: testing}}|==Performance==
  
We also have an MPI version compiled with MVAPICH/0.9.9
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WRITE_PERFORMANCE_TESTING_RESULTS_HERE
$module load intel/10.1 mvapich/0.9.9 mrbayes
 
  
{{#if: {{#var: exe}}|==How To Run==
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|}}
WRITE INSTRUCTIONS ON RUNNING THE ACTUAL BINARY|}}
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<!--Faq-->
{{#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==
 
{{#if: {{#var: faq}}|==FAQ==
 
*'''Q:''' **'''A:'''|}}
 
*'''Q:''' **'''A:'''|}}
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<!--Citation-->
 
{{#if: {{#var: citation}}|==Citation==
 
{{#if: {{#var: citation}}|==Citation==
If you publish research that uses {{{app}}} you have to cite it as follows:
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If you publish research that uses {{#var:app}} you have to cite it as follows:
WRITE CITATION HERE
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 +
WRITE_CITATION_HERE
 +
 
 
|}}
 
|}}
 +
<!--Installation-->
 +
{{#if: {{#var: installation}}|==Installation==
 +
See the [[{{PAGENAME}}_Install]] page for {{#var: app}} installation notes.|}}
 +
<!--Turn the Table of Contents and Edit paragraph links ON/OFF-->
 +
__NOTOC____NOEDITSECTION__

Latest revision as of 15:03, 11 April 2022

Description

mrbayes website  

MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. MrBayes uses Markov chain Monte Carlo (MCMC) methods to estimate the posterior distribution of model parameters.

Environment Modules

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

System Variables

  • HPC_MRBAYES_DIR - installation directory

Additional Information

For MPI jobs
  • As a rule of thumb ntasks should be set to the total number of chains (MrBayes default is 4 chains * 2 runs = 8 chains)
  • As long as the number of cores is under 12, it is best to use a single node ("SBATCH --nodes=1") where nodes are physical computers as that will keep all communication within a single node.