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, Christoph Heibl, Daniel Lawson, Vincent Lefort, Pierre Legendre, Jim Lemon, Yvonnick Noel, Johan Nylander, Rainer Opgen-Rhein, Andrei-Alin Popescu, Klaus Schliep, 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 in
13 a phylogenetic framework, ancestral character analyses, analyses of
14 diversification and macroevolution, computing distances from allelic
15 and nucleotide data, reading and writing nucleotide sequences, and
16 several tools such as Mantel's test, minimum spanning tree,
17 generalized skyline plots, graphical exploration of phylogenetic
18 data (alex, trex, kronoviz), estimation of absolute evolutionary
19 rates and clock-like trees using mean path lengths and penalized
20 likelihood. Phylogeny estimation can be done with the NJ, BIONJ, ME,
21 MVR, SDM, and triangle methods, and several methods handling
22 incomplete distance matrices (NJ*, BIONJ*, MVR*, and the
23 corresponding triangle method). Some functions call external
24 applications (PhyML, Clustal, T-Coffee, Muscle) whose results are
27 URL: http://ape.mpl.ird.fr/