PROML
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
