PROML

PROML is an implementation of Phylip package. It infers an unrooted phylogeny from amino acid sequences using maximum likelihood.  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

• To use PROML, upload your data in Phylip interleaved format format.
• Resources: Phylip 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 > proml

Input File

• Use the file elong_alpha_20_phylip.phy as a test input file. This example has the elongation factor alpha gene, downloaded from GenBank for 20 species.

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 the following output files:
  • output.txt – the text output of the analysis
  • runlog.txt – a log of parameters used in the analysis
  • treefile.newick.phy – the tree file in Newick format
  • treefile.svg – a SVG tree image generated by TreeVector
  • treefile.png – a PNG version of the tree image
  • TreeVector.html – a downloadable HTML form to render the tree in TreeVector using different options

More Information

• proml
• Seqboot
• Consense