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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DNANJ

DNANJ is an implementation of neighbor-joining in the Phylip package. It infers phylogenetic trees using the neighbor-joining method method.  The application accepts as input a multiple DNA 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

All files are located in the Community Data directory of the iPlant Discovery Environment at the following path:

Community Data > iplantcollaborative > example_data > dnanj

Input File

  • Use the file M3297_20_phylip.phy as a test input file. This example is a randomly selected subset of 20 taxa from TreeBase character matrix M3297 from "Brassicaceae phylogeny inferred from phytochrome A and ndhF sequence data: tribes and trichomes revisited".

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 an in plain text format and a tree file in newick format as output. Additional outputs are a run log, two tree images and an html file.

More Information