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