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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PhyML reconstructs phylogenetic trees using Maximum Likelihood.

Quick Start

  • To use PhyML, upload your data in Phylip format.
  • Resources: documentation 

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 > phyml > data

Input File(s)

  • Requires an alignment file an Phylip format.  May be a DNA (nt) or AA (amino acid) alignment
  • Test data: Use aln.phy as a test input file.

Parameters Used in App

  • You will need to specify if the alignment file is DNA (nt) or AA.  By default AA is selected

Output File(s)

  • Expected outputs:
    • aln.phy_phyml_stats.txt
    • aln.phy_phyml_tree.txt

Tool Source for App


  1. ★★★★☆ Very nice app! (by nicole)

  2. ★★★★★ null (by zpierce)

  3. ★★★★★ Wonderful! (by elyons)