PhyML

Owned by mhelmke
Last updated: Jun 03, 2015 by kkennedy

PhyML

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