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\name{ape-package}
\alias{ape-package}
\alias{ape}
\docType{package}
\title{
Analyses of Phylogenetics and Evolution
}
\description{
\pkg{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
\code{library(help = ape)}.
More information on \pkg{ape} can be found at \url{http://ape-package.ird.fr/}.
}
\author{
Emmanuel Paradis, Ben Bolker, Julien Claude, Hoa Sien Cuong, Richard
Desper, Benoit Durand, Julien Dutheil, Olivier Gascuel, Christoph
Heibl, Daniel Lawson, Vincent Lefort, Pierre Legendre, Jim Lemon,
Yvonnick Noel, Johan Nylander, Rainer Opgen-Rhein, Andrei-Alin
Popescu, Klaus Schliep, Korbinian Strimmer, Damien de Vienne
Maintainer: Emmanuel Paradis <Emmanuel.Paradis@ird.fr>
}
\references{
Paradis, E. (2012) \emph{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. \emph{Bioinformatics},
\bold{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. \emph{Bioinformatics}, \bold{28}, 1536--1537.
Paradis, E. and Schliep, K. (2019) ape 5.0: an environment for modern
phylogenetics and evolutionary analyses in R. \emph{Bioinformatics},
\bold{35}, 526--528.
}
\keyword{package}
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