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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PROTPARS

PROTPARS is an implementation of Phylip package. It infers an unrooted phylogeny from amino acid sequences using the maximum parsimony method.  The application accepts as input a multiple sequence alignment in Phylip interleaved format. If bootstrapping is selected, a user specified number of bootstrap replicates will be sampled from the input alignment and the consensus tree will be reported.

Quick Start

Test Data

All files are located in the Community Data directory of the iPlant Discovery Environment at the following path:

Community Data > iplantcollaborative > example_data > protpars

Input File

Parameters Used in Application

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

  • Default parameters only, no further configuration needed.

Output Files

  • Expect an in plain text format and a tree file in newick format as output. Additional files include a runlog, 2 image files (png and svg) and an html file.

More Information