CACE (Continuous Ancestral Character Estimation)
CACE infers ancestral state of a continuous trait in a phylogeny using Maximum Likelihood.
- To use CACE, upload your tree (newick, nexus) and trait matrix (csv).
- Resources: documentation
All files are located in the Community Data directory of the iPlant Discovery Environment at the following path:
Community Data > iplantcollaborative > example_data > cace
(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.
- 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: