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: 5.8-1
Depends: R (≥ 3.2.0)
Imports: nlme, lattice, graphics, methods, stats, utils, parallel, Rcpp (≥ 0.12.0), digest
LinkingTo: Rcpp
Suggests: gee, expm, igraph, phangorn, xml2
Published: 2024-12-16
DOI: 10.32614/CRAN.package.ape
Author: Emmanuel Paradis ORCID iD [aut, cre, cph], Simon Blomberg ORCID iD [aut, cph], Ben Bolker ORCID iD [aut, cph], Joseph Brown ORCID iD [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 ORCID iD [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 ORCID iD [aut, cph], Federico Marotta [aut, cph], Eric Marcon ORCID iD [aut, cph], Rosemary McCloskey ORCID iD [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>
BugReports: https://github.com/emmanuelparadis/ape/issues
License: GPL-2 | GPL-3
URL: https://github.com/emmanuelparadis/ape
NeedsCompilation: yes
Citation: ape citation info
Materials: README NEWS
In views: Environmetrics, Phylogenetics
CRAN checks: ape results

Documentation:

Reference manual: ape.pdf
Vignettes: Drawing Phylogenies (source, R code)
Moran's I (source, R code)
Random Topology (source, R code)

Downloads:

Package source: ape_5.8-1.tar.gz
Windows binaries: r-devel: ape_5.8-1.zip, r-release: ape_5.8-1.zip, r-oldrel: ape_5.8-1.zip
macOS binaries: r-release (arm64): ape_5.8-1.tgz, r-oldrel (arm64): ape_5.8-1.tgz, r-release (x86_64): ape_5.8-1.tgz, r-oldrel (x86_64): ape_5.8-1.tgz
Old sources: ape archive

Reverse dependencies:

Reverse depends: Anaconda, apex, aphylo, BAMMtools, BarcodingR, Canopy, caper, cati, cauphy, Claddis, clstutils, coalescentMCMC, convevol, corHMM, ctpm, dispRity, distory, diversitree, FD, geiger, hisse, ips, JNplots, jrich, MCMCglmm, MCMCtreeR, MiSPU, MonoPhy, motmot, MPSEM, MSCquartets, MSCsimtester, mvMORPH, nichevol, nodeSub, OUwie, paleoDiv, paleotree, pegas, perspectev, pez, phangorn, phyclust, PhylogeneticEM, phylolm, phylotools, phyloTop, phytools, picante, quiddich, recluster, RNeXML, Rphylopars, rwty, sangeranalyseR, sensiPhy, strap, surface, TESS, treats, treebase, treedater, TreeSim, treespace, treestartr, TreeTools, VDJgermlines, windex
Reverse imports: abdiv, adaptiveGPCA, adegenet, adephylo, adiv, admtools, alakazam, animalcules, AnnotationBustR, aPCoA, Apoderoides, arakno, avotrex, BAT, beastier, beautier, betapart, BIEN, bioregion, bioseq, bivariatemaps, bnpsd, BoSSA, CALANGO, canaper, ccfindR, chemodiv, cloneRate, CluMSID, clusterExperiment, coil, colordistance, CommEcol, compcodeR, concatipede, copyseparator, covid19.analytics, CRABS, DAISIEprep, DAMOCLES, dartR, dartR.base, DCLEAR, DDD, ddtlcm, debar, DHARMa, divent, do3PCA, dowser, ecoregime, entropart, EnvNJ, EpiModel, epm, evobiR, evolqg, evolvability, evolved, EvoPhylo, fastreeR, file2meco, FishPhyloMaker, fishtree, FossilSim, FuncDiv, funspace, genBaRcode, geneHapR, geneplast, geneplast.data, geomorph, ggmuller, ggrasp, ggtree, ggtreeSpace, GIFT, glinvci, GmicR, GOCompare, gquad, gromovlab, GUniFrac, HACSim, haplotypes, harrietr, HGC, hilldiv, hillR, HMPTrees, Hmsc, holobiont, homals, HybridMicrobiomes, iCAMP, iCellR, idar, immunarch, indelmiss, iNEXT.3D, iNEXT.beta3D, infercnv, insect, ipADMIXTURE, itol.toolkit, jackalope, LinTInd, longreadvqs, LorMe, MACER, MAGNAMWAR, markophylo, MesKit, mFD, MGnifyR, mia, miaViz, MicrobiomeBenchmarkData, microbiomeDataSets, MicrobiotaProcess, microeco, MiscMetabar, ML.MSBD, MLVSBM, mmodely, MSA2dist, msaR, multilaterals, mvSLOUCH, NicheBarcoding, nLTT, nodiv, NormalyzerDE, NST, numbat, occCite, OmaDB, ontophylo, openPrimeR, oposSOM, oppr, orthGS, outbreaker2, packFinder, paco, palaeoverse, PathoStat, PBD, pcmabc, PCMBase, PCPS, philr, phyext2, phylepic, phylobase, phylocanvas, phylogram, phylopairs, phylopath, PhyloProfile, phyloraster, phyloregion, phylosem, phyloseq, phylosignal, phylter, phyr, PhySortR, Plasmidprofiler, POMS, pooledpeaks, poolfstat, popkin, poppr, POSTm, POUMM, poweRbal, ppgm, primerTree, prioritizr, PVR, qlcData, QSutils, Quartet, RAINBOWR, rapidphylo, ratematrix, restez, RevGadgets, Revticulate, rhierbaps, rKOMICS, Rogue, rotl, rr2, rrnni, RRphylo, RRPP, Rtapas, Rtropical, scAnnotatR, scBubbletree, scFeatures, scistreer, scMultiSim, secsse, SeqFeatR, sharpshootR, shazam, shinyTempSignal, shinyWGD, sidier, SigTree, singleCellTK, SiPhyNetwork, sitePath, slendr, slouch, SpaceMarkers, spANOVA, SPARTAAS, spider, STEPCAM, STraTUS, stylo, Sysrecon, systemPipeTools, tanggle, tapnet, tbea, TBRDist, tidytree, TML, TransPhylo, TreeAndLeaf, treebalance, treeclimbR, treeDA, TreeDiagram, TreeDist, treeio, treekoR, treenomial, TreeSearch, TreeSimGM, treesliceR, treestats, treestructure, TreeSummarizedExperiment, vcfR, VERSO, Xplortext, yatah
Reverse suggests: ade4, adespatial, aphid, aqp, asnipe, babette, brms, BSTZINB, castor, CongreveLamsdell2016, CTNote, DAISIE, data.tree, deeptime, dendextend, divraster, dynamicSDM, ecolottery, ecospat, ecotraj, ENMTools, enveomics.R, FAVA, fido, FinePop, ggimage, ggmsa, gllvm, glmmTMB, GLSME, hagis, harmonicmeanp, hierfstat, HSAUR, HSAUR2, HSAUR3, idpr, igraph, insight, jSDM, kmer, lingtypology, mcbette, mdendro, meconetcomp, mecoturn, metadat, metafor, metagear, miaSim, msa, MVA, netdiffuseR, nosoi, OptCirClust, orthogene, ouch, outbreaks, paleobuddy, pctax, phylocomr, phylotate, Platypus, plotbb, polysat, rbiom, rdiversity, rehh, rncl, rphylopic, RPointCloud, rSWeeP, RVAideMemoire, sand, scrm, Seurat, shipunov, SoilTaxonomy, spiralize, supportR, symmoments, systemPipeShiny, taxlist, TextMiningGUI, tidygraph, tidysq, TiPS, TotalCopheneticIndex, tracerer, universalmotif, vhica, warbleR
Reverse enhances: clue

Linking:

Please use the canonical form https://CRAN.R-project.org/package=ape to link to this page.