ape (3.0-9)

Analyses of Phylogenetics and Evolution.


ape provides functions for reading, writing, plotting, and manipulating phylogenetic trees, analyses of comparative data in a phylogenetic framework, ancestral character analyses, analyses of diversification and macroevolution, computing distances from allelic and nucleotide data, reading and writing nucleotide sequences, and several tools such as Mantel's test, minimum spanning tree, generalized skyline plots, graphical exploration of phylogenetic data (alex, trex, kronoviz), estimation of absolute evolutionary rates and clock-like trees using mean path lengths 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). Some functions call external applications (PhyML, Clustal, T-Coffee, Muscle) whose results are returned into R.

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, Andrei-Alin Popescu, Klaus Schliep, Korbinian Strimmer, Damien de Vienne

License: GPL (>= 2)

Uses: lattice, nlme, gee, expm
Reverse depends: AbSim, adegenet, adephylo, adhoc, adiv, apex, aptg, apTreeshape, auteur, BAMMtools, BarcodingR, bayou, BBMV, bcool, BioGeoBEARS, BPEC, Canopy, caper, cati, Claddis, coalescentMCMC, CommEcol, convevol, corHMM, DAMOCLES, DDD, dispRity, distory, diversitree, ecospat, epibase, expoTree, FD, geiger, geomorph, GUniFrac, HAP.ROR, harmonicmeanp, hisse, HMPTrees, homals, HyPhy, idar, ips, iteRates, jaatha, jrich, kernelPop, laser, maticce, MCMCglmm, MCMCtreeR, metaboGSE, metricTester, MiSPU, Momocs, MonoPhy, motmot, motmot.2.0, MPSEM, msap, MSCquartets, mvMORPH, mvSLOUCH, nichevol, nodiv, oposSOM, outbreaker, OUwie, paleotree, pastis, pcrcoal, pegas, perspectev, pez, phangorn, phybase, phybreak, phyclust, phyext, phyloclim, PhylogeneticEM, phylolm, phylosim, phylotools, phyloTop, phytools, picante, poppr, PVR, RADami, RAM, rase, RBrownie, recluster, Reol, rmetasim, RNeXML, Rphylopars, rwty, sensiPhy, SeqFeatR, sidier, spider, strataG, StructFDR, surface, TESS, treebase, treedater, treelet, TreePar, treeplyr, treescape, TreeSim, TreeSimGM, treespace, treestartr, TreeTools, VDJgermlines, windex
Reverse suggests: ade4, adegenet, adephylo, adespatial, ALA4R, aphid, apTreeshape, aqp, asnipe, babette, balance, brms, CongreveLamsdell2016, data.tree, dcGOR, dendextend, EcoGenetics, ecolottery, enveomics.R, FinePop, gamclass, ggimage, ggmsa, GLSME, harmonicmeanp, hierfstat, HSAUR, HSAUR2, HSAUR3, igraph, jaatha, kmer, kmeRs, markophylo, metagear, multicross, MVA, netdiffuseR, nosoi, ouch, outbreaks, paco, phylocomr, phylogram, phylotate, phylotools, polysat, prioritizr, rbiom, rdiversity, readGenalex, rehh, rncl, rphast, sand, scrm, shipunov, speciesgeocodeR, structSSI, subniche, symmoments, taxlist, tidygraph, TotalCopheneticIndex, tracerer, treeDA, vhica, warbleR
Reverse enhances: clue

Released almost 7 years ago.