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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CACE (Continuous Ancestral Character Estimation)

CACE infers ancestral state of a continuous trait in a phylogeny using Maximum Likelihood.

Quick Start

  • To use CACE, upload your tree (newick, nexus) and trait matrix (csv).
  • 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 > cace

Input Files

(taken from Ackerly, D. 2009. Conservatism and diversification of plant functional traits: Evolutionary rates versus phylogenetic signal. PNAS 106:19699--19706.)

  • Use Acer-leaf_seed.csv as a test input file for traits.
  • Use Acer-tree.txt 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 File

  • Expect multiple files as output, including a tree with named internal nodes in Newick format and plotted in PDF. For the example data above, the following results should be expected:
    • dataout.csv
    • In.LeafArea.cm2_nodes.txt
    • In.LeafArea.cm2_out.txt
    • In.LeafArea.cm2_plot.pdf
    • In.LeafArea.cm2_tree.txt

Tool Source for App

1 Comment

  1. ★★★★☆ null (by smckay)