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:
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- Atmosphere
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This is RAxML version 8.2.9 on the CyVerse UK hardware (12 cpus, 256 GB per job). It is software to determine the best phylogenetic tree based on a sequence alignment using Maximum Likelihood (ML) statistical modeling. See for more info.

Quick Start

  • The only necessary parameters are the input file, algorithm and model, for which the defaults should be ok.
  • Depending on your data, make sure to select the right model (Nucleotide, Protein, Binary).
  • All parameters have their command line option mentioned, for easy searching in the manual

Test Data


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

Input File(s)

Use at least:

  • An alignment file

The example files also show a DNA / protein combined example file with a pairing partitions file.

For explanation of the other possible files see the manual.

Output Files

Depends on the action, but at least:

  • RAxML.log - job log file
  • RAxML.out - job output messages
  • RAxML.err - job error messages
  • RAxML_parsimonyTree.out - Starting tree used by RAxML
  • RAxML_result.out - depending on the algorithm and options, the best phylogenetic tree found by RAxML 
  • RAxML_bestTree.out - the best phylogenetic tree found
  • RAxML_info.out - RAxML specific output messages
  • RAxML_log.out - RAxML general log
  • RAxML_result.out - the result of your analysis (usually the same as the bestTree file)

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

Tool Source for App


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