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)
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RAxML

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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 http://sco.h-its.org/exelixis/web/software/raxml/index.html 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

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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 -> 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

https://github.com/stamatak/standard-RAxML

 

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