Difference between revisions of "MrBayes"
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[[Category:Software]][[Category:Phylogenetics]] | [[Category:Software]][[Category:Phylogenetics]] | ||
− | + | {|<!--Main settings - REQUIRED--> | |
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− | <!--Main settings - REQUIRED--> | ||
|{{#vardefine:app|mrbayes}} | |{{#vardefine:app|mrbayes}} | ||
|{{#vardefine:url|http://mrbayes.sourceforge.net/}} | |{{#vardefine:url|http://mrbayes.sourceforge.net/}} | ||
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|{{#vardefine:exe|}} <!--Present manual instructions for running the software --> | |{{#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| | + | |{{#vardefine:pbs|}} <!--Enable PBS script wiki page link--> |
|{{#vardefine:policy|}} <!--Enable policy section --> | |{{#vardefine:policy|}} <!--Enable policy section --> | ||
|{{#vardefine:testing|}} <!--Enable performance testing/profiling section --> | |{{#vardefine:testing|}} <!--Enable performance testing/profiling section --> | ||
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<!--Description--> | <!--Description--> | ||
{{#if: {{#var: url}}| | {{#if: {{#var: url}}| | ||
− | {{App_Description|app={{#var:app}}|url={{#var:url}}}}|}} | + | {{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. | ||
− | + | In addition to the official MrBayes distribution, a modified version that uses the Gamma-Dirichlet and Inverse Gamma-Dirichlet priors for branch lengths (Rannala et al. in press; Zhang et al. 2012). This also includes the two exponential priors on internal and external branch lengths described by Yang & Rannala (2005) and Yang (2007). Please see [http://abacus.gene.ucl.ac.uk/software.html Ziheng Yang's site] for more information and citations. The modified version is only installed for openmpi and is called mb_Dirichlet. To run this version, simply replace mb with mb_Dirichlet in the examples below. | |
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− | The | ||
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− | {{#if: {{#var: exe}}|== | + | <!--Modules--> |
+ | ==Required Modules== | ||
+ | [[Modules|modules documentation]] | ||
+ | ===Serial=== | ||
+ | *{{#var:app}} | ||
+ | ===Parallel (OpenMP)=== | ||
+ | *intel | ||
+ | *{{#var:app}} | ||
+ | ===Parallel (OpenMPI)=== | ||
+ | *intel | ||
+ | *openmpi | ||
+ | *{{#var:app}} | ||
+ | ==System Variables== | ||
+ | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory | ||
+ | <!--Additional--> | ||
+ | {{#if: {{#var: exe}}|==Additional Information== | ||
WRITE INSTRUCTIONS ON RUNNING THE ACTUAL BINARY|}} | WRITE INSTRUCTIONS ON RUNNING THE ACTUAL BINARY|}} | ||
{{#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==|}} | ||
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For MPI jobs: Remember that the total number of cores cannot be greater than the total number of chains MrBayes is using. For example, if you have 2 runs, each with 4 chains, the maximum number of cores to request is 2*4=8 cores. As long as the number of cores is under 12, it is best to keep nodes=1 (nodes = physical machines) as that will keep all communication within a single node. If you need more than 12 cores, you will probably want to add :infiniband to the request. (e.g. nodes=4:ppn=8:infiniband). | For MPI jobs: Remember that the total number of cores cannot be greater than the total number of chains MrBayes is using. For example, if you have 2 runs, each with 4 chains, the maximum number of cores to request is 2*4=8 cores. As long as the number of cores is under 12, it is best to keep nodes=1 (nodes = physical machines) as that will keep all communication within a single node. If you need more than 12 cores, you will probably want to add :infiniband to the request. (e.g. nodes=4:ppn=8:infiniband). | ||
+ | <!-- | ||
{{#fileAnchor: mrbayes.MPI.pbs}} | {{#fileAnchor: mrbayes.MPI.pbs}} | ||
Download raw source of the [{{#fileLink: mrbayes.MPI.pbs}} mrbayes.MPI.pbs] | Download raw source of the [{{#fileLink: mrbayes.MPI.pbs}} mrbayes.MPI.pbs] | ||
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#PBS -l walltime=01:00:00 | #PBS -l walltime=01:00:00 | ||
# | # | ||
− | + | # Change to the directory from which the job was submitted | |
− | #Change to the directory | + | # |
cd $PBS_O_WORKDIR | cd $PBS_O_WORKDIR | ||
− | + | # | |
− | #Use modules to | + | # Use modules to configure your environment for mrbayes |
− | module load intel | + | # |
− | module load openmpi | + | module load intel |
+ | module load openmpi | ||
module load mrbayes | module load mrbayes | ||
− | + | # | |
− | # | + | # Run MrBayes using the command line from documentation. |
− | + | # | |
− | + | mpiexec mb my_nexus.nex | |
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− | #Run MrBayes using the command line from documentation. | ||
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</source> | </source> | ||
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#PBS -l walltime=01:00:00 | #PBS -l walltime=01:00:00 | ||
# | # | ||
− | + | # Change to the directory from which the job was submitted | |
− | #Change to the directory | + | # |
cd $PBS_O_WORKDIR | cd $PBS_O_WORKDIR | ||
− | + | # | |
− | #Use modules to | + | # Use modules to configure your environment for mrbayes |
− | + | # | |
module load mrbayes | module load mrbayes | ||
− | + | # | |
+ | # launch the executable | ||
+ | # | ||
mb my_nexus.nex | mb my_nexus.nex | ||
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</source> | </source> | ||
− | {{#if: {{#var: policy}}|==Usage | + | --> |
+ | {{#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== |
Revision as of 21:23, 6 December 2019
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.
In addition to the official MrBayes distribution, a modified version that uses the Gamma-Dirichlet and Inverse Gamma-Dirichlet priors for branch lengths (Rannala et al. in press; Zhang et al. 2012). This also includes the two exponential priors on internal and external branch lengths described by Yang & Rannala (2005) and Yang (2007). Please see Ziheng Yang's site for more information and citations. The modified version is only installed for openmpi and is called mb_Dirichlet. To run this version, simply replace mb with mb_Dirichlet in the examples below.
Required Modules
Serial
- mrbayes
Parallel (OpenMP)
- intel
- mrbayes
Parallel (OpenMPI)
- intel
- openmpi
- mrbayes
System Variables
- HPC_MRBAYES_DIR - installation directory
For MPI jobs: Remember that the total number of cores cannot be greater than the total number of chains MrBayes is using. For example, if you have 2 runs, each with 4 chains, the maximum number of cores to request is 2*4=8 cores. As long as the number of cores is under 12, it is best to keep nodes=1 (nodes = physical machines) as that will keep all communication within a single node. If you need more than 12 cores, you will probably want to add :infiniband to the request. (e.g. nodes=4:ppn=8:infiniband).