Emmanuel Paradis <paradis@isem.univ-montp2.fr>
Korbinian Strimmer <strimmer@stat.uni-muenchen.de>
Julien Claude <claude@isem.univ-montp2.fr>
Yvonnick Noel <noel@univ-lille3.fr>
Ben Bolker <bolker@zoo.ufl.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, or the
population parameter theta based on various approaches.

Emmanuel Paradis <paradis@isem.univ-montp2.fr>
Korbinian Strimmer <strimmer@stat.uni-muenchen.de>
Julien Claude <claude@isem.univ-montp2.fr>
Gangolf Jobb <gangolf@treefinder.de>
Yvonnick Noel <noel@univ-lille3.fr>
Ben Bolker <bolker@zoo.ufl.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, 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.

Ben Bolker, Julien Claude, Benoit Durand,
Julien Dutheil, Gangolf Jobb, Jim Lemon, Yvonnick Noel,
Johan Nylander, Rainer Opgen-Rhein, Emmanuel Paradis,
Korbinian Strimmer
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.