DACE (Discrete Ancestral Character Estimation)

DACE infers the ancestral state of a discrete trait in a phylogeny using Maximum Likelihood.

Quick Start

• To use DACE, upload your tree (newick, nexus) and trait matrix (cvs) files.
• Resources:/wiki/spaces/Events/pages/242199797

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 > dace

Input File(s)

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

• Use lobelioids.csv  as a test input file for traits.
• Use lobelioids-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.

OR

• Use these parameters within the DE app interface:
  • parameter name - value/setting
  • parameter name - value/setting

Output File(s)

• Expect multiple files as output, including a tree with named internal nodes in Newick format and plotted in PDF.

Tool Source for App

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