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 on CyVerse UK

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This is MrBayes version  3.2.6 on the CyVerse UK hardware (12 cpus, 256 GB per job). It is software for Bayesian analysis of molecular sequences using MCMC. See http://mrbayes.sourceforge.net/manual.php for more info.

Quick Start

  • This is a fairly simple app in terms of inputs and outputs, all it needs is a Nexus file with a sequence alignment and a .bb file with a MrBayes block in it; this contains a sequence alignment and all options necessary for the program. See the example file in the example data. Also see the detailed guide in the manual (http://mrbayes.sourceforge.net/mb3.2_manual.pdf) pp 109.

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_uk

Input File(s)

Only two files are necessary, the Nexus file with the alignment and the .bb file with the MrBayes block.

Output Files

  • mrbayes.err, mrbayes.log, mrbayes.out - standard error, out and log
  • filename.runX.p - files showing the substitution model parameters for each run and chain
  • filename.runX.t - files showing the tree topologies found in those runs
  • filename.ckp - checkpoint files to resume your analysis if stopped

Other files may appear depending on your model, partitions, options etc...

Tool Source for App

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

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