Ape provides functions for reading, writing, plotting,
and manipulating phylogenetic trees, analyses of comparative data
in a phylogenetic framework, analyses of diversification and
macroevolution, computing distances from allelic and nucleotide
data, reading nucleotide sequences, and several tools such as
Mantel's test, computation of minimum spanning tree, the population
parameter theta based on various approaches, nucleotide diversity,
generalized skyline plots, estimation of absolute evolutionary rates
and clock-like trees using non-parametric rate smoothing, conversion
of APE trees to and from hclust objects and for classifying genes in
trees using the Klastorin-Misawa-Tajima approach. Phylogeny estimation
can be done with the NJ and ML methods.

Emmanuel Paradis <paradis@isem.univ-montp2.fr>,
Korbinian Strimmer <strimmer@stat.uni-muenchen.de>,
Julien Claude <claude@isem.univ-montp2.fr>,
Gangolf Jobb <gangolf.deletethis@treefinder.de>,
Rainer Opgen-Rhein <opgen@stat.uni-muenchen.de>,
Julien Dutheil <julien.dutheil@univ-montp2.fr>,
Yvonnick Noel <noel@univ-lille3.fr>,
Ben Bolker <bolker@zoo.ufl.edu>,
Jim Lemon <jim@bitwrit.com.au>

Emmanuel Paradis <paradis@isem.univ-montp2.fr>,
Korbinian Strimmer <strimmer@stat.uni-muenchen.de>,
Julien Claude <claude@isem.univ-montp2.fr>,
Gangolf Jobb <gangolf.deletethis@treefinder.de>,
Rainer Opgen-Rhein <opgen@stat.uni-muenchen.de>,
Julien Dutheil <julien.dutheil@univ-montp2.fr>,
Yvonnick Noel <noel@univ-lille3.fr>,
Ben Bolker <bolker@zoo.ufl.edu>,
Jim Lemon <jim@bitwrit.com.au>,
Benoît Durand <b.durand@alfort.AFSSA.FR>,
Johan Nylander <nylander@scs.fsu.edu>

Ape provides functions for reading, writing, plotting,
and manipulating phylogenetic trees, analyses of comparative data
in a phylogenetic framework, analyses of diversification and
macroevolution, computing distances from allelic and nucleotide
data, reading nucleotide sequences, and several tools such as
Mantel's test, computation of minimum spanning tree, the population
parameter theta based on various approaches, nucleotide diversity,
generalized skyline plots, estimation of absolute evolutionary rates
and clock-like trees using non-parametric rate smoothing and penalized
likelihood, classifying genes in trees using the Klastorin-Misawa-Tajima
approach. Phylogeny estimation can be done with the NJ and ML methods.