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RAxML Start Tree 8.2.11

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For additional information on this tool, please consult the RAxML manual.

Test Data

Use the alignment file

49

as test data. It can be accessed by navigating to:

'Community Data'>iplantcollaborative>example_data/RAxML/raxml-RFdistancestarttree

Parameters Used in App

When the app is run in the Discovery Environment, use the following parameters with the above input file to get the output provided in the next section below.

• Run the test analysis using the following parameters:
  
  1. type of start tree: faster random parsimony
  2. substitution model (-m): GRTCAT
  3. Output file base name: 49-1
  4. Random integer to use as random parsimony seed (-p): leave blank to allow the app to generate a random see for you.

Output File(s)

• Expect the following output files:
  • .agave.log: log of activity by the Agave API that ran the app
  • 49: the input alignment
  • 49.reduced: an alignment file with undetermined columns removed
  • RAxML_parsimonyTree.49-1: the output of the program. A start tree for further analysis.
  • RAxML_info.49-1: Information about the model and algorithm used and how the program was called.
  • $longrandomstring.err: standard error
  • $longrandomstring.out: standard output

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