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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Maintenance Notice for July 23, 2019

On Tuesday, July 23, CyVerse will be performing a Ceph storage upgrade from 11:00 AM to 5:00 PM MST. This is not expected to cause disruptions to the affected services. The services to be upgraded include:
- CyVerse authentication (CAS), which provides authentication to CyVerse web applications, e.g., the Discovery Environment and User Portal
- Atmosphere
- Any "Powered by CyVerse" systems or other hosted systems on Tombstone Cloud (please ask if you are unsure)
- Hosted Jupyter Notebooks on

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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 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 ( pp 109.

Test Data


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

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