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
9 Maintainer: Emmanuel Paradis <Emmanuel.Paradis@mpl.ird.fr>
11 Suggests: gee, nlme, lattice
13 Description: ape provides functions for reading, writing, plotting,
14 and manipulating phylogenetic trees, analyses of comparative data
15 in a phylogenetic framework, analyses of diversification and
16 macroevolution, computing distances from allelic and nucleotide
17 data, reading nucleotide sequences, and several tools such as
18 Mantel's test, computation of minimum spanning tree, the population
19 parameter theta based on various approaches, nucleotide diversity,
20 generalized skyline plots, estimation of absolute evolutionary rates
21 and clock-like trees using mean path lengths, non-parametric rate
22 smoothing and penalized likelihood, classifying genes in trees using
23 the Klastorin-Misawa-Tajima approach. Phylogeny estimation can be done
24 with the NJ, BIONJ, ME, and ML methods.
26 URL: http://pbil.univ-lyon1.fr/R/ape/