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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Parser-3.0.20

 

Parser-3.0.20  is an Agave app for running parse, which is required to run ExaML (Exascale Maximum Likelihood code for phylogenetic inference on supercomputers using MPI). Parse converts an alignment file in relaxed phylip format (as used for RAxML) into a binary file format that can be read by ExaML. The main reason for this is to allow ExaML to read this file faster and not waste any valuable parallel computing time for this simple pre-processing task.

The parser-3.0.20  app runs on the Stampede2 supercomputer at the Texas Advanced Computing center. It uses an executable from the examl repo, version 3.0.20, built using Makefile.SSE3.gcc. The maximum run time is two hours, but this should be enough to parse even very large alignments.

Please cite the following paper when using parsers-3.0.30 and ExaML:

A. Kozlov, A.J. Aberer, A. Stamatakis: “ExaML Version 3: A Tool for Phylogenomic Analyses on Supercomputer”. In Bioinformatics (2015) doi: 10.1093/bioinformatics/btv184

Quick Start

  • To use parser-3.0.20, upload your alignment in relaxed PHYLIP format (interleaved, no name length restrictions)
  • Resources: 

Inputs

parser-3.0.20  requires an input alignment in relaxed PHYLIP format. In addition, if your analysis includes partitions, you must upload a partition file. For the syntax of this file please consult the RAxML manual.

 

Test Data

Use the nucleotide alignment

49 

and the partion file

49.model 

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

'Community Data'>iplantcollaborative>example_data/ExaML/parse

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. substitution model/type of data: DNA
    2. Output file base name: 49

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.binary: the output of the program. Use this file as input to ExaML
    • 49.model: the input partition model
    • RAxML_info.49: Information about the model and algorithm used and how the program was called. This file also contains an estimate of the memory required to run your ExaML analysis.
    • $longrandomstring.err: standard error
    • $longrandomstring.out: standard output

Tool Source

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