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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RAxML Robinson-Foulds Distance 8.2.11

 

raxml-RFdistance-8.2.11 is an Agave app for using RAxML to compute all pairwise Robinson-Foulds distances among a set of phylogentic trees.

The raxml-RFdistance-8.2.11 app runs on the Stampede2 supercomputer at the Texas Advanced Computing center. It uses an executable from the RAxML repo, version 8.2.11, built using Makefile.AVX2.gcc. The maximum run time is two hours, but this should be enough to calculate distances for most sets of trees.

Please cite the following paper when using raxml-RFdistance-8.2.11 and RAxML:

A. Stamatakis: "RAxML Version 8: A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies". In Bioinformatics, 2014, open access.

Quick Start

  • To use raxml-RFdistance-8.2.11, you must first generate a batch of trees (e.g., using raxml-starttree-8.2.11) and concatenating all trees into a single file. There must be a carriage return after each tree. You can do this using the "Concatenate multiple files" app in the DE, or with a text editor.
  • Resources: 

Inputs

raxml-RFdistance-8.2.11 requires a text file containing a concatenated list of trees to be compared. For additional information on this tool, please consult the RAxML manual.

Test Data

Use the nucleotide text file

49_10_trees.txt

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

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

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. substitution model: GTRCAT
    2. Output file base name: 49-10

Output File(s)

  • Expect the following output files:
    • .agave.log: log of activity by the Agave API that ran the app
    • 49_10_trees.txt: the input text file with concatenated trees
    • RAxML_RF-Distances.49-10: the output of the program. Contains a list of all pairwise distances.
    • RAxML_info.49-10: Information about the model and algorithm used and how the program was called.
    • $longrandomstring.err: standard error
    • $longrandomstring.out: standard output

Tool Source

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