ape: Analyses of Phylogenetics and Evolution

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 DNA sequences, reading and writing nucleotide sequences as well as importing from BioConductor, and several tools such as Mantel's test, 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, dating trees with non-contemporaneous sequences, translating DNA into AA sequences, and assessing sequence alignments. 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.

Version: 5.4-1
Depends: R (≥ 3.2.0)
Imports: nlme, lattice, graphics, methods, stats, tools, utils, parallel, Rcpp (≥ 0.12.0)
LinkingTo: Rcpp
Suggests: gee, expm, igraph
Published: 2020-08-13
Author: Emmanuel Paradis ORCID iD [aut, cre, cph], Simon Blomberg ORCID iD [aut, cph], Ben Bolker ORCID iD [aut, cph], Joseph Brown [aut, cph], Santiago Claramunt ORCID iD [aut, cph], Julien Claude ORCID iD [aut, cph], Hoa Sien Cuong [aut, cph], Richard Desper [aut, cph], Gilles Didier ORCID iD [aut, cph], Benoit Durand [aut, cph], Julien Dutheil ORCID iD [aut, cph], RJ Ewing [aut, cph], Olivier Gascuel [aut, cph], Thomas Guillerme ORCID iD [aut, cph], Christoph Heibl ORCID iD [aut, cph], Anthony Ives [aut, cph], Bradley Jones ORCID iD [aut, cph], Franz Krah ORCID iD [aut, cph], Daniel Lawson ORCID iD [aut, cph], Vincent Lefort [aut, cph], Pierre Legendre ORCID iD [aut, cph], Jim Lemon [aut, cph], Guillaume Louvel [aut, cph], Eric Marcon ORCID iD [aut, cph], Rosemary McCloskey [aut, cph], Johan Nylander [aut, cph], Rainer Opgen-Rhein [aut, cph], Andrei-Alin Popescu [aut, cph], Manuela Royer-Carenzi [aut, cph], Klaus Schliep ORCID iD [aut, cph], Korbinian Strimmer ORCID iD [aut, cph], Damien de Vienne ORCID iD [aut, cph]
Maintainer: Emmanuel Paradis <Emmanuel.Paradis at ird.fr>
License: GPL-2 | GPL-3
URL: http://ape-package.ird.fr/
NeedsCompilation: yes
Citation: ape citation info
Materials: NEWS
In views: Environmetrics, Genetics, Graphics, Phylogenetics
CRAN checks: ape results

Downloads:

Reference manual: ape.pdf
Vignettes: Moran's I
Package source: ape_5.4-1.tar.gz
Windows binaries: r-devel: ape_5.4-1.zip, r-release: ape_5.4-1.zip, r-oldrel: ape_5.4-1.zip
macOS binaries: r-release: ape_5.4-1.tgz, r-oldrel: ape_5.4-1.tgz
Old sources: ape archive

Reverse dependencies:

Reverse depends: AbSim, adhoc, apex, apTreeshape, BAMMtools, BarcodingR, BBMV, BDMMAcorrect, Canopy, caper, cati, Claddis, clstutils, coalescentMCMC, CommEcol, convevol, corHMM, dispRity, distory, diversitree, ecospat, FD, geiger, GUniFrac, hisse, HyPhy, idar, ips, iteRates, jrich, MCMCglmm, MCMCtreeR, metaboGSE, MiSPU, motmot, MPSEM, MSCquartets, mvMORPH, nichevol, OUwie, paleotree, pastis, pegas, perspectev, pez, phangorn, phyclust, phyloclim, PhylogeneticEM, phylolm, phylotools, phyloTop, phytools, picante, quiddich, rase, recluster, RNeXML, Rphylip, Rphylopars, rwty, sensiPhy, strap, StructFDR, TESS, treebase, treedater, TreePar, treeplyr, TreeSim, treespace, treestartr, TreeTools, VDJgermlines, windex
Reverse imports: abdiv, adaptiveGPCA, adegenet, adephylo, adiv, alakazam, animalcules, AnnotationBustR, aPCoA, beastier, beautier, betapart, BIEN, bioseq, bite, BoSSA, BPEC, brranching, ccfindR, CluMSID, clusterExperiment, CNull, coil, colordistance, CommT, contact, DAMOCLES, dartR, DDD, debar, DHARMa, entropart, EpiModel, evobiR, evolqg, expands, fishtree, FossilSim, genBaRcode, geneplast, geomedb, geomorph, ggmuller, ggrasp, ggtree, GmicR, gquad, graphscan, gromovlab, HACSim, haplotypes, harrietr, HierDpart, hilldiv, hillR, HMPTrees, Hmsc, homals, HTSSIP, iCAMP, iCellR, indelmiss, infercnv, insect, ipADMIXTURE, jackalope, kdetrees, liayson, LINC, MAGNAMWAR, markophylo, metacoder, metagenomeFeatures, MicrobiotaProcess, missSBM, ML.MSBD, msap, msaR, multilaterals, mvSLOUCH, nLTT, nodiv, NormalyzerDE, NST, OmaDB, openPrimeR, oposSOM, oppr, outbreaker2, ouxy, packFinder, paco, PathoStat, PBD, pcmabc, PCMBase, PCPS, perfectphyloR, philr, phyext2, PhyInformR, phylobase, phylocanvas, phylogram, phyloland, PhyloMeasures, phylopath, PhyloProfile, phyloregion, phyloseq, phylosignal, phyr, PhySortR, PIGShift, Plasmidprofiler, poppr, POUMM, primerTree, prioritizr, PVR, QSutils, Quartet, RAINBOWR, RAM, ratematrix, rhierbaps, rotl, RPANDA, RPS, rr2, RRphylo, RRPP, secsse, selac, SeqFeatR, sharpshootR, shazam, sidier, SigTree, singleCellTK, sitePath, slingshot, slouch, spANOVA, spider, STEPCAM, STraTUS, stylo, supraHex, taxize, TBRDist, tidytree, TransPhylo, TreeAndLeaf, TreeDist, treeio, treeman, treenomial, TreeSearch, TreeSimGM, treestructure, TreeSummarizedExperiment, universalmotif, vcfR, yatah
Reverse suggests: ade4, adespatial, ALA4R, aphid, aqp, asnipe, babette, balance, brms, CongreveLamsdell2016, curatedMetagenomicData, DAISIE, data.tree, dcGOR, dendextend, ecolottery, ENMTools, enveomics.R, FinePop, genphen, ggimage, ggmsa, GLSME, harmonicmeanp, hierfstat, HSAUR, HSAUR2, HSAUR3, igraph, kmer, kmeRs, metagear, msa, multicross, MVA, netdiffuseR, nosoi, ouch, outbreaks, phylocomr, phylotate, polysat, rbiom, rdiversity, rehh, rncl, safedata, sand, scrm, Seurat, shipunov, subniche, symmoments, systemPipeR, TextMiningGUI, tidygraph, TotalCopheneticIndex, tracerer, treeDA, vhica, warbleR
Reverse enhances: clue

Linking:

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