Description: Provides tools to identify and visualize branches in a phylogenetic tree that are significantly responsive to some intervention, taking as primary inputs a phylogenetic tree (of class phylo) and a data frame (or matrix) of corresponding tip (OTU) labels and p-values.

Title: Functions to determine significantly responsive branches of
phylogenetic trees and produce colored plots both in FigTree
Description: SigTree takes a phylogenetic tree (of class phylo) and a data frame (or matrix) of corresponding tip labels and p-values and determines the significance of the branches (families of p-values) and plots the tree with colored branches (corresponding to families) according to the levels of significance,  Also produces a CSV file with the p-values of all of the branches as well as which tips belong to which branches.  Finally, it exports a file that can be opened in FigTree that produces a colored plot (colored branches according to the significance of corresponding groups of p-values) with p-value annotations.
Depends: ape, phylobase, phyext, RColorBrewer, phyloseq
Packaged: 2013-08-14 22:27:15 UTC; John Stevens

Title: Determine significantly responsive branches in phylogenetic
Description: SigTree takes a phylogenetic tree (of class phylo) and a data frame (or matrix) of corresponding tip labels and p-values and determines the significance of the branches (families of p-values) and plots the tree with colored branches (corresponding to families) according to their levels of significance.  Also produces a CSV file with the p-values of all of the branches as well as which tips belong to which branches.  Finally, it exports a file that can be opened in FigTree that produces a colored plot (colored branches according to their significance of corresponding groups of p-values) with p-value annotations.
Packaged: 2013-12-28 00:48:16 UTC; John R Stevens

Title: Identify and visualize significantly responsive branches in a
Imports: ape, phyext, RColorBrewer, phyloseq
Packaged: 2014-05-23 21:34:42 UTC; John R Stevens
Author: John R. Stevens [aut, cre, ths, cph] (www.stat.usu.edu/jrstevens),
Todd R. Jones [aut, cph] (www.toddrjones.com)