CONTRAST

CONTRAST adjusts trait values for phylogenetic signal to determine if traits are correlated by function or by descent from a common ancestor.

Quick Start

• To use CONTRAST, upload your data in Nexus format.
• 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 > contrast

(taken from David D. Ackerly and Peter B. Reich, “Convergence and correlations among leaf size and function in seed plants: a comparative test using independent contrasts,” Am. J. Bot. 86, no. 9 (September 1, 1999): 1272-1281.)

Inputs

• Use leaf.fel as a test input file for traits.
• Use leaf-tree.nwk as a test input file for a tree.

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

• Expect as output a list of correlation coefficients for the pair-wise contrasts, the individual contrasts, or a graphical output of the pair-wise correlations. With the example data above, the following files are generated:
  • output.txt (contrasts and regressions)
  • runlog.txt (this contains information about the parameters passed to the tool)

Tool Source for App

...