Analyses of Phylogenetics and Evolution
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.
Paradis, E. and Schliep, K. (2019) ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R. Bioinformatics, 35, 526--528.