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, ME, MVR, SDM, and triangle methods, and several methods handling incomplete distance matrices (NJ*, BIONJ*, MVR*, and the corresponding triangle method).
| Version: | 2.8 |
| Depends: | R (≥ 2.6.0) |
| Imports: | gee, nlme, lattice |
| Suggests: | gee |
| Published: | 2011-10-24 |
| 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 |
| Maintainer: | Emmanuel Paradis <Emmanuel.Paradis at ird.fr> |
| License: | GPL (≥ 2) |
| URL: | http://ape.mpl.ird.fr/ |
| Citation: | ape citation info |
| In views: | Environmetrics, Genetics, Graphics, Phylogenetics |
| CRAN checks: | ape results |
| Package source: | ape_2.8.tar.gz |
| MacOS X binary: | ape_2.8.tgz |
| Windows binary: | ape_2.8.zip |
| Reference manual: | ape.pdf |
| Vignettes: |
Moran's I |
| News/ChangeLog: | NEWS |
| Old sources: | ape archive |
| Reverse depends: | adephylo, auteur, bcool, caper, distory, diversitree, FD, geiger, HMPTrees, homals, iteRates, kernelPop, laser, MCMCglmm, motmot, oposSOM, OUwie, paleotree, pcrcoal, pegas, phangorn, phybase, phyclust, phyext, phylobase, phyloclim, phylosim, phylotools, phytools, picante, rmetasim, spider, treebase, treelet, TreePar, TreeSim |
| Reverse imports: | apTreeshape, BoSSA, OUwie, pcrcoal, phylosim, pmc |
| Reverse suggests: | ade4, adegenet, apTreeshape, aqp, hierfstat, HSAUR, HSAUR2, MVA, ouch, rphast |
| Reverse enhances: | clue |