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GainsboroOrangeVISIBLE ONLY TO STAFF - CONTENT HIDDEN FOR DEPRECATED APP

MrBayes 3.2.1 MPI Basic App

Community rating: ?????

MrBayes is a program for Bayesian inference and model choice using Markov chain Monte Carlo (MCMC) methods to estimate the posterior distribution of model parameters.

Ronquist, F., M. Teslenko, P. van der Mark, D. Ayres, A. Darling, S. Hohna, B. Larget, L. Liu, M. A. Suchard, and J. P. Huelsenbeck. 2011. MrBayes 3.2: Efficient Bayesian phylogenetic inference and model choice across a large model space. Systematic Biology 61(3): 539-542.

Quick Start

To use MrBayes, upload your data in Nexus format.
Your Nexus file must include a properly formatted character matrix plus a complete MrBayes block.
- Unlike the desktop version of MrBayes, this app is not interactive. You must include all parameters and commands (including mcmc, sumt, and sump) in the MrBayes block in your Nexus file. Any unspecified parameters will use the default values specified in the MrBayes manual.
- See test data (below) for examples of properly formatted Nexus files.
- See the MrBayes manual for more information on how to create a properly formatted Nexus file.
This MPI app is designed to run on the Lonestar Supercomputer at the Texas Advance Computing Center, which has twelve cores per node. Therefor, you must set the total number of chains to a multiple of 12 (e.g., 2 runs of six chains, 3 runs of 4 chains, 4 runs of six chains). You must specify the number of run and chains in your MrBayes block. In addition, you will be asked to input the total number of chains by the application interface.
There is a 24 hour limit on all jobs submitted via this app. This means that very large matrices (many taxa or many characters) will probably not reach convergence in the time allotted. If the number of generations is set very high and your job does not finish in 24 hours, you will not get any output. This app is best used with small to medium sized matrices.
Resources: MrBayes online documentation

Test Data

Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> MrBayes

Input File(s)

Use primates-run.nex or cynmix-run.nex from the directory above as test input.

Parameters Used in App

When the app is run in the Discovery Environment, use the following parameters with the above input file(s) to get the output provided in the next section below.

All parameters must be entered in the MrBayes block in the input Nexus file. In addition, you must enter the total number of chains.
For the example files above, keep the default number of chains as 12.

Output File(s)

Expect as output a set of files prefixed with the name of the input file. The exact output files will depend on the commands entered, but should include at least:
- Input.nex.mcmc
- Input.nex.run1.p – text file with substitution model parameters from run 1
- Input.nex.run1.t – Nexus file with topology and branch lengths of sampled trees from run 1
- Input.nex.run2.p – text file substitution model parameters from run 2
- Input.nex.run2.t – Nexus file with topology and branch lengths of sampled trees from run 2
- Job_name.err – standard error
- Job_name.out – standard output
If you enter primates-run.nex as your input file, you should get the following 15 files as output:
- primates-run.nex
- primates-run.nex.con.tre
- primates-run.nex.lstat
- primates-run.nex.mcmc
- primates-run.nex.parts
- primates-run.nex.pstat
- primates-run.nex.run1.p
- primates-run.nex.run1.t
- primates-run.nex.run2.p
- primates-run.nex.run2.t
- primates-run.nex.trprobs
- primates-run.nex.tstat
- primates-run.nex.vstat
- Job_name.err – standard error
- Job_name.out – standard output

Tool Source for App

http://mrbayes.sourceforge.net/index.php

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Teslenko, P. van der Mark, D. Ayres, A. Darling, S. Hohna, B. Larget, L. Liu, M. A. Suchard, and J. P. Huelsenbeck. 2011. MrBayes 3.2: Efficient Bayesian phylogenetic inference and model choice across a large model space. ","type":"text"},{"text":"Systematic Biology 61(3): 539-542","type":"text","marks":[{"type":"link","attrs":{"href":"http://sysbio.oxfordjournals.org/content/early/2012/03/02/sysbio.sys029.short"}}]},{"text":".","type":"text"}]},{"type":"heading","attrs":{"level":2},"content":[{"text":"Quick Start","type":"text"}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"To use MrBayes, upload your data in Nexus format.","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Your Nexus file must include a properly formatted character matrix plus a complete MrBayes block.","type":"text"}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Unlike the desktop version of MrBayes, this app is not interactive. You must include all parameters and commands (including mcmc, sumt, and sump) in the MrBayes block in your Nexus file. 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MrBayes 3.2.1 MPI Basic App (archived)

The system on which this app runs is no longer available. The replacement app for MrBayes 3.2.3 is available at MrBayes_mpi_basic-3.2.3.