Difference between revisions of "MrBayes"
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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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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 | + | 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. |
<!--Modules--> | <!--Modules--> | ||
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*{{#var:app}} | *{{#var:app}} | ||
==System Variables== | ==System Variables== | ||
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
<!--Additional--> | <!--Additional--> | ||
{{#if: {{#var: exe}}|==Additional Information== | {{#if: {{#var: exe}}|==Additional Information== | ||
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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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mb my_nexus.nex | mb my_nexus.nex | ||
</source> | </source> | ||
| − | + | --> | |
{{#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)|}} | WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)|}} | ||
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).