ape provides functions for reading, writing, manipulating, analysing, and simulating phylogenetic trees and DNA sequences, computing DNA distances, translating into AA sequences, estimating trees with distance-based methods, and a range of methods for comparative analyses and analysis of diversification. Functionalities are also provided for programming new phylogenetic methods.
The complete list of functions can be displayed with
library(help = ape).
More information on ape can be found at http://ape-package.ird.fr/.
Paradis, E. (2012) Analysis of Phylogenetics and Evolution with R (Second Edition). New York: Springer.
Paradis, E., Claude, J. and Strimmer, K. (2004) APE: analyses of phylogenetics and evolution in R language. Bioinformatics, 20, 289--290.
Popescu, A.-A., Huber, K. T. and Paradis, E. (2012) ape 3.0: new tools for distance based phylogenetics and evolutionary analysis in R. Bioinformatics, 28, 1536-1537.