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.
- To use PROTPARS, upload your data in Phylip interleaved format format.
- Resources: Phylip documentation
All files are located in the Community Data directory of the iPlant Discovery Environment at the following path:
Community Data > iplantcollaborative > example_data > protpars
- 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.
- 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.