The applications listed here are available for use in the Discovery Environment and are documented in: Discovery Environment Manual.

Discovery Environment Applications List

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MrBayes 3.2.3 MPI Basic App

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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 two files in Nexus format:
    1. A nexus file containing the data (i.e. taxa and characters). The taxa and character data may be in a single block or in two separate blocks. This file must have one of the following extensions: .nex, NEX, .nexus, .NEXUS, .Nexus
    2. A nexus file containing a MrBayes Block.
      • It must begin with an execute command for the data files (see example input files, below, and the MrBayes manual).
      • Your MrBayes block must specify a total of 16 chains (either 4 runs of 4 chains or 2 runs of 8 chains). The job will fail if you do not include this.
      • 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 properly formatted Nexus files.
  • This is a High Performance Computing (HPC) application designed to run in parallel on 16 cores on the Stampede supercomputer at the Texas Advance Computing Center. Because of this, it will only run if you have specified 16 chains total in your MrBayes block.
  • There is a 48 hour limit on all jobs submitted via this app. This means that very large matrices (many taxa or many characters) may not reach convergence in the time allotted. If the number of generations is set very high and your job does not finish in 48  hours, you will not get any output. Therefore, it is recommended that you first submit and MrBayes block with a small number of generations (e.g., 1 million) to determine how many generations your analysis can get through in 48 hours and then set up your main analysis accordingly.
    • Although MrBayes is check-pointable, the checkpointing function has not been implemented in this app yet. If there is demand, it may be added in the future.
  • Remember, because this is an HPC app, the wait time once the job is submitted may be longer than you are used to.

Test Data

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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.nex (data)  primates-run.nex  (MrBayes block) 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.

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.nex and primates-run.nex as your input files, 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

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