SigTree: Identify and visualize significantly responsive branches in a phylogenetic tree

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.

Version: 1.7
Imports: ape, phyext, RColorBrewer, phyloseq
Published: 2014-12-10
Author: John R. Stevens and Todd R. Jones
Maintainer: John R. Stevens <john.r.stevens at usu.edu>
License: GPL-3
NeedsCompilation: yes
Citation: SigTree citation info
Materials: NEWS
In views: Phylogenetics
CRAN checks: SigTree results

Downloads:

Reference manual: SigTree.pdf
Vignettes: SigTree Tutorial Vignette
Package source: SigTree_1.7.tar.gz
Windows binaries: r-devel: SigTree_1.7.zip, r-release: SigTree_1.7.zip, r-oldrel: SigTree_1.7.zip
OS X Snow Leopard binaries: r-release: not available, r-oldrel: SigTree_1.7.tgz
OS X Mavericks binaries: r-release: not available
Old sources: SigTree archive