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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These apps have been deprecated, because the systems on which they ran was decommissioned.


RAxML implements a rapid maximum likelihood-based inference of phylogenetic trees from nucleotide or amino acid multiple sequence alignments. The phylip_interleaved.phy output of the Muscle App in the Discovery Environment is suitable input for this analysis. RAxML now accepts FASTA files as input as well.

RAxML-small 8.2.3

RAxML-small-8.2.3: This version of RAxML runs on the Stampede supercomputer at the Texas Advanced Computing center. It was compiled using the PTHREAD-SSE3 option. The small app is limited to 2 hours run time on one node (16 cores), which generally provides a short wait time on the queue. This app will work best with small input files and a limited number of boostrap replicates, and can be used for scripted workflows that require several small analyses to run in parallel.

RAxML-medium 8.2.3

RAxML-medium-8.2.3: This version of RAxML runs on the Stampede supercomputer at the Texas Advanced Computing center. It was compiled using the PTHREAD-SSE3 option. While this version will run much faster than a desktop version, it is limited to 48 hours run time on one node with 16 cores. Therefore, it should work best with medium-sized analyses. For small analyses, use RAxML-small-8.2.3, which generally have a shorter wait time on the queue. Very large runs will not finish in 48 hours.

We are considering making a large version of the software available. If this would be of use to you, please post a request at http://ask.iplantcollaborative.org.

Quick Start

  • To use RAxML-8.2.3 small or medium, upload your data in relaxed PHYLIP format (interleaved, no name length restrictions) or FASTA.
  • Resources:

Inputs

RAxML requires an input alignment in PHYLIP or FASTA format. In addition, you may input any of the following file types:

  • multiple model (partition) file (-q)
  • protein substitution model file (-P)
  • single tree file (-t)
  • multiple tree file (-z)
  • multifurcating constraint tree (-g)
  • binary constraint tree (-r)
  • binary model parameter file (-R)
  • secondary structure file (-S)
  • column weight file (-a)
  • exclude file name (-E)
  • quartet grouping file (-Y)

Please see the RAxML manual for guidance on how and when to use these input files. Most input files can only be used with specific options (see Parameters used in app, below). For input files, you do not need to specify flags (e.g., -q) as the app automatically adds them.

For some additional example files and hand-on exercises, see http://sco.h-its.org/exelixis/web/software/raxml/hands_on.html. The example data needed for these exercises is in the RAxML community data folder listed in the section below.

Test Data

Use the nucleotide alignment dna.phy as test data.  It can be accessed by navigating to :

'Community Data'>iplantcollaborative>example_data>raxml-8.2.3>dna.phy

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 default parameters for:
    1. substitutionModel = GTRGAMMA
    2. numberOfRuns=100
    3. outputFileName=nwk
    4. parsimonyRandomSeed=123445 (can change this - it will not affect results)
    5. additionalOptions={leave blank}

You SHOULD NOT include flags for options 1-4, as the program automatically adds them.

You can include any other valid RAxML options as a string using the "additionalOptions" parameter. These options will be appended to the end of the required options 1-4. When specifying additional options, you MUST include the flag, as specified in the RAxML manual. If your options require an input file, be sure to include it in the Inputs section.

Do not use the number of threads (-T) option with this app.

Output File(s)

  • Expect the following output files:
    • dna.phy: copy of the input file
    • agave-$longrandomstring.err: standard error
    • agave-$longrandomstring.out: standard output
    • RAxML_info.nwk: Information about the model and algorithm used and how RAxML was called. The final GAMMA-based likelihood(s) as well as the alpha shape

      parameter(s) are printed to this file.

    • RAxML_log.nwk.RUN.0 - RAxML_log.nwk.RUN.99: A file that prints out the time, likelihood value of the current tree after each

      iteration of the search algorithm. In the last line it also contains the final likelihood value of the final tree topology of each run.

    • RAxML_parsimonyTree.nwk.RUN.0 - RAxML_parsimonyTree.nwk.RUN.99: Contains the randomized parsimony starting tree if the program has not been provided a starting tree.
    • RAxML_result.nwk.RUN.0 - RAxML_result.nwk.RUN.99: Contains the final tree topology of the current run.
    • RAxML_bestTree.nwk: Contains the best-scoring ML tree of a thorough ML analysis.

Tool Source

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