ape (2.6-2)
Analyses of Phylogenetics and Evolution.
http://ape.mpl.ird.fr/
http://cran.r-project.org/web/packages/ape
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, generalized skyline plots, estimation of absolute evolutionary rates and clock-like trees using mean path lengths, non-parametric rate smoothing and penalized likelihood. Phylogeny estimation can be done with the NJ, BIONJ, and ME methods.
Maintainer:
Emmanuel Paradis
Author(s): 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, Klaus Schliep, Korbinian Strimmer, Damien de Vienne
License: GPL (>= 2)
Uses: gee, lattice, nlme, gee
Reverse depends: adegenet, adephylo, apTreeshape, auteur, bcool, caper, coalescentMCMC, corHMM, distory, diversitree, epibase, FD, geiger, geomorph, GUniFrac, HAP.ROR, HMPTrees, homals, HyPhy, iteRates, jaatha, kernelPop, laser, maticce, MCMCglmm, Momocs, motmot, msap, oposSOM, outbreaker, OUwie, pcrcoal, pegas, phangorn, phybase, phyclust, phyext, phyloclim, phylolm, phylosim, phylotools, phytools, picante, poppr, PVR, RBrownie, recluster, Reol, rmetasim, sidier, spider, surface, TESS, treebase, treelet, TreePar, TreeSim
Reverse suggests: ade4, adegenet, adephylo, apTreeshape, aqp, gamclass, hierfstat, HSAUR, HSAUR2, igraph, MVA, ouch, phylotools, rphast
Reverse enhances: clue
Released over 2 years ago.
