4 Title: Analyses of Phylogenetics and Evolution
5 Author: Emmanuel Paradis, Ben Bolker, Julien Claude, Hoa Sien Cuong, Richard Desper, Benoit Durand, Julien Dutheil, Olivier Gascuel, Gangolf Jobb, Christoph Heibl, Daniel Lawson, Vincent Lefort, Pierre Legendre, Jim Lemon, Yvonnick Noel, Johan Nylander, Rainer Opgen-Rhein, Korbinian Strimmer, Damien de Vienne
6 Maintainer: Emmanuel Paradis <Emmanuel.Paradis@ird.fr>
9 Imports: gee, nlme, lattice
11 Description: ape provides functions for reading, writing, plotting,
12 and manipulating phylogenetic trees, analyses of comparative data
13 in a phylogenetic framework, analyses of diversification and
14 macroevolution, computing distances from allelic and nucleotide
15 data, reading nucleotide sequences, and several tools such as
16 Mantel's test, computation of minimum spanning tree, the population
17 parameter theta based on various approaches, nucleotide diversity,
18 generalized skyline plots, estimation of absolute evolutionary rates
19 and clock-like trees using mean path lengths, non-parametric rate
20 smoothing and penalized likelihood. Phylogeny estimation can be done
21 with the NJ, BIONJ, and ME methods.
23 URL: http://ape.mpl.ird.fr/