Determine significantly responsive branches in phylogenetic trees

Description

SigTree is a package of functions to determine significant response of branches of phylogenetic trees and produce colored plots both in R and (via exported .tre file) FigTree. plotSigTree 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 (as families of p-values) and plots the tree with colored branches (corresponding to families) according to the level of significance of the branch. export.inherit produces a CSV file (or data frame) with the p-values for all branches as well as which tips belong to which branches. export.figtree exports a .tre file that can be opened in FigTree that produces a colored plot (with colors according to the significance of corresponding branches) with p-value annotations.

Details

For more information, see the documentation for plotSigTree, export.inherit, and export.figtree.

To access the tutorial document for this package, type in R: vignette("SigTree")

Author(s)

John R. Stevens and Todd R. Jones

Maintainer: John R. Stevens <john.r.stevens@usu.edu>

References

Stevens J.R., Jones T.R., Lefevre M., Ganesan B., and Weimer B.C. (2015) "SigTree: identifying and visualizing significantly responsive branches in a phylogenetic tree" (Manuscript in preparation).

Jones T.R. (2012) "SigTree: An Automated Meta-Analytic Approach to Find Significant Branches in a Phylogenetic Tree" (2012). MS Thesis, Utah State University, Department of Mathematics and Statistics. http://digitalcommons.usu.edu/etd/1314

FigTree is available at http://tree.bio.ed.ac.uk/software/figtree/.

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