Difference between revisions of "MrBayes"

Latest revision as of 12:28, 19 August 2022

Description

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.

@@ Line 1: / Line 1: @@
-MrBayes has been installed on the cluster. We currently have two different versions installed:
+[[Category:Software]][[Category:Biology]][[Category:Phylogenetics]]
+{|<!--CONFIGURATION: REQUIRED-->
+|{{#vardefine:app|mrbayes}}
+|{{#vardefine:url|http://nbisweden.github.io/MrBayes}}
+<!--CONFIGURATION: OPTIONAL (|1}} means it's ON)-->
+|{{#vardefine:conf|}}           <!--CONFIGURATION-->
+|{{#vardefine:exe|1}}            <!--ADDITIONAL INFO-->
+|{{#vardefine:job|}}            <!--JOB SCRIPTS-->
+|{{#vardefine:policy|}}         <!--POLICY-->
+|{{#vardefine:testing|}}       <!--PROFILING-->
+|{{#vardefine:faq|}}             <!--FAQ-->
+|{{#vardefine:citation|}}       <!--CITATION-->
+|{{#vardefine:installation|}} <!--INSTALLATION-->
+|}
+<!--BODY-->
+<!--Description-->
+{{#if: {{#var: url}}|
+{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}
- /apps/mrbayes/bin/mb-mpi   <- Parallel Version
+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.
- /apps/mrbayes/bin/mb       <- Single processor version
+<!--Modules-->
+==Environment Modules==
+Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
+==System Variables==
+* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
+<!--Configuration-->
+{{#if: {{#var: conf}}|==Configuration==
+See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.
+|}}
+<!--Run-->
+{{#if: {{#var: exe}}|==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.
+|}}
+<!--Job Scripts-->
+{{#if: {{#var: job}}|==Job Script Examples==
+See the [[{{PAGENAME}}_Job_Scripts]] page for {{#var: app}} Job script examples.
+|}}
+<!--Policy-->
+{{#if: {{#var: policy}}|==Usage Policy==
+WRITE USAGE POLICY HERE (Licensing, usage, access).
+|}}
+<!--Performance-->
+{{#if: {{#var: testing}}|==Performance==
+WRITE_PERFORMANCE_TESTING_RESULTS_HERE
+|}}
+<!--Faq-->
+{{#if: {{#var: faq}}|==FAQ==
+*'''Q:''' **'''A:'''|}}
+<!--Citation-->
+{{#if: {{#var: citation}}|==Citation==
+If you publish research that uses {{#var:app}} you have to cite it as follows:
+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__