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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Ninja

Ninja is a neighbor-joining method for the construction of large phylogenetic trees.

Quick Start

  • To use Ninja, upload your data in FASTA format for alignments or PHYLIP format for pairwise distance matrices.
  • 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 > ninja

Input File(s)

Parameters Used in App

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 File(s)

  • Expect a tree file in Newick format as output

Tool Source