Difference between revisions of "MrBayes"
Jump to navigation
Jump to search
(New page: MrBayes has been installed on the cluster. We currently have two different versions installed: /apps/mrbayes/bin/mb-mpi <- Parallel Version /apps/mrbayes/bin/mb <- Single proces...) |
Moskalenko (talk | contribs) m (Text replacement - "#uppercase" to "uc") |
||
| (31 intermediate revisions by 6 users not shown) | |||
| Line 1: | Line 1: | ||
| − | + | __NOTOC__ | |
| + | __NOEDITSECTION__ | ||
| + | [[Category:Software]][[Category:Phylogenetics]] | ||
| + | {|<!--Main settings - REQUIRED--> | ||
| + | |{{#vardefine:app|mrbayes}} | ||
| + | |{{#vardefine:url|http://mrbayes.sourceforge.net/}} | ||
| + | |{{#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--> | ||
| + | |{{#vardefine:policy|}} <!--Enable policy section --> | ||
| + | |{{#vardefine:testing|}} <!--Enable performance testing/profiling section --> | ||
| + | |{{#vardefine:faq|}} <!--Enable FAQ section --> | ||
| + | |{{#vardefine:citation|}} <!--Enable Reference/Citation section --> | ||
| + | |} | ||
| + | <!-- ######## Template Body ######## --> | ||
| + | <!--Description--> | ||
| + | {{#if: {{#var: url}}| | ||
| + | {{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}} | ||
| − | + | 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. | ||
| + | |||
| + | <!--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|}} | ||
| + | {{#if: {{#var: conf}}|==Configuration== | ||
| + | See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.|}} | ||
| + | {{#if: {{#var: pbs}}|==PBS Script Examples==|}} | ||
| + | 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}} | ||
| + | Download raw source of the [{{#fileLink: mrbayes.MPI.pbs}} mrbayes.MPI.pbs] | ||
| + | <source lang=bash> | ||
| + | #!/bin/bash | ||
| + | # | ||
| + | #PBS -N mrbayes | ||
| + | #PBS -M <your e-mail> | ||
| + | #PBS -m abe | ||
| + | #PBS -o mb.$PBS_JOBID.out | ||
| + | #PBS -e mb.$PBS_JOBID.err | ||
| + | #PBS -l nodes=1:ppn=8 | ||
| + | #PBS -l pmem=500mb | ||
| + | #PBS -l walltime=01:00:00 | ||
| + | # | ||
| + | # Change to the directory from which the job was submitted | ||
| + | # | ||
| + | cd $PBS_O_WORKDIR | ||
| + | # | ||
| + | # Use modules to configure your environment for mrbayes | ||
| + | # | ||
| + | module load intel | ||
| + | module load openmpi | ||
| + | module load mrbayes | ||
| + | # | ||
| + | # Run MrBayes using the command line from documentation. | ||
| + | # | ||
| + | mpiexec mb my_nexus.nex | ||
| + | </source> | ||
| + | |||
| + | |||
| + | |||
| + | '''Script for serial (single core) MrBayes job:''' | ||
| + | {{#fileAnchor: mrbayes.serial.pbs}} | ||
| + | Download raw source of the [{{#fileLink: mrbayes.serial.pbs}} mrbayes.serial.pbs] | ||
| + | <source lang=bash> | ||
| + | #!/bin/bash | ||
| + | # | ||
| + | #PBS -N mrbayes | ||
| + | #PBS -M <your e-mail> | ||
| + | #PBS -m abe | ||
| + | #PBS -o mb.$PBS_JOBID.out | ||
| + | #PBS -e mb.$PBS_JOBID.err | ||
| + | #PBS -l nodes=1:ppn=1 | ||
| + | #PBS -l pmem=500mb | ||
| + | #PBS -l walltime=01:00:00 | ||
| + | # | ||
| + | # Change to the directory from which the job was submitted | ||
| + | # | ||
| + | cd $PBS_O_WORKDIR | ||
| + | # | ||
| + | # Use modules to configure your environment for mrbayes | ||
| + | # | ||
| + | module load mrbayes | ||
| + | # | ||
| + | # launch the executable | ||
| + | # | ||
| + | mb my_nexus.nex | ||
| + | </source> | ||
| + | --> | ||
| + | {{#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== | ||
| + | *'''Q:''' **'''A:'''|}} | ||
| + | {{#if: {{#var: citation}}|==Citation== | ||
| + | If you publish research that uses {{{app}}} you have to cite it as follows: | ||
| + | WRITE CITATION HERE | ||
| + | |}} | ||
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).