Package: ape 5.8-0.2

Emmanuel Paradis

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.

Authors:Emmanuel Paradis [aut, cre, cph], Simon Blomberg [aut, cph], Ben Bolker [aut, cph], Joseph Brown [aut, cph], Santiago Claramunt [aut, cph], Julien Claude [aut, cph], Hoa Sien Cuong [aut, cph], Richard Desper [aut, cph], Gilles Didier [aut, cph], Benoit Durand [aut, cph], Julien Dutheil [aut, cph], RJ Ewing [aut, cph], Olivier Gascuel [aut, cph], Thomas Guillerme [aut, cph], Christoph Heibl [aut, cph], Anthony Ives [aut, cph], Bradley Jones [aut, cph], Franz Krah [aut, cph], Daniel Lawson [aut, cph], Vincent Lefort [aut, cph], Pierre Legendre [aut, cph], Jim Lemon [aut, cph], Guillaume Louvel [aut, cph], Eric Marcon [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 [aut, cph], Korbinian Strimmer [aut, cph], Damien de Vienne [aut, cph]

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ape/json (API)
NEWS

# Install 'ape' in R:
install.packages('ape', repos = c('https://phylotastic.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/emmanuelparadis/ape/issues

Uses libs:
  • openblas– Optimized BLAS
  • c++– GNU Standard C++ Library v3
Datasets:

On CRAN:

339 exports 52 stars 11.08 score 4 dependencies 560 dependents 918 mentions 11.3k scripts 72.9k downloads

Last updated 2 months agofrom:6d4fb54677. Checks:OK: 9. Indexed: no.

TargetResultDate
Doc / VignettesOKAug 21 2024
R-4.5-win-x86_64OKAug 21 2024
R-4.5-linux-x86_64OKAug 21 2024
R-4.4-win-x86_64OKAug 21 2024
R-4.4-mac-x86_64OKAug 21 2024
R-4.4-mac-aarch64OKAug 21 2024
R-4.3-win-x86_64OKAug 21 2024
R-4.3-mac-x86_64OKAug 21 2024
R-4.3-mac-aarch64OKAug 21 2024

Exports:.compressTipLabel.PlotPhyloEnv.uncompressTipLabel[.DNAbinAAsubstabbreviateGenusaceadd.scale.baradditivealexall.equal.DNAbinall.equal.phyloalviewarecompatibleas.AAbinas.AAbin.characteras.alignmentas.bitsplitsas.bitsplits.prop.partas.character.AAbinas.character.DNAbinas.DNAbinas.DNAbin.alignmentas.DNAbin.characteras.DNAbin.listas.evonetas.evonet.phyloas.hclust.phyloas.igraph.evonetas.igraph.phyloas.list.AAbinas.list.DNAbinas.matchingas.matching.phyloas.matrix.DNAbinas.network.evonetas.network.phyloas.networx.evonetas.phyDat.AAbinas.phyloas.phylo.evonetas.phylo.formulaas.phylo.hclustas.phylo.matchingas.phylo.phylogas.prop.partaxisPhylobalancebase.freqbd.extbd.timebinaryPGLMMbinaryPGLMM.simbind.treebionjbionjsbiplot.pcoabirthdeathbitsplitsboot.phyloBOTHlabelsbranching.timesbydirc.DNAbinCADM.globalCADM.postcbind.DNAbincheckAlignmentcheckLabelcheckValidPhylocherrychronoMPLchronoplchronoschronos.controlcircular.plotcladewisecladogram.plotclustalclustalomegacoalescent.intervalscollapse.singlescollapsed.intervalscompar.cheverudcompar.geecompar.lynchcompar.oucomparePhylocomplementcompute.brlencompute.brtimeconsensuscophenetic.phylocophyloplotcorBlombergcorBrowniancorGrafencorMartinscorPagelcorphylocorrelogram.formulacountBipartitionsdbddbdTimedefdegreedel.colgapsonlydel.gapsdel.rowgapsonlydelta.plotdeviance.acedi2multidi2multi.multiPhylodi2multi.phylodist.aadist.dnadist.genedist.nodesdist.topodiversi.gofdiversi.timediversity.contrast.testDNAbin2indeldndsdrawSupportOnEdgesdrop.fossildrop.tipdrop.tip.multiPhylodrop.tip.phylodyuleedgelabelsedgeseditFileExtensionsefastatsestimate.datesestimate.muevonetewLassoextract.cladeextract.popsizefancyarrowsfastme.balfastme.olsfind.skyline.epsilonfloating.pie.aspFtabgammaStatGC.contentgetAnnotationsGenBankgetMRCAhas.singleshowmanytreesimage.AAbinimage.DNAbinis.binaryis.binary.multiPhylois.binary.phylois.binary.treeis.compatibleis.compatible.bitsplitsis.monophyleticis.rootedis.rooted.multiPhylois.rooted.phylois.ultrametricis.ultrametric.multiPhylois.ultrametric.phylokeep.tipkeep.tip.multiPhylokeep.tip.phylokronovizlabel2tablelabels.DNAbinladderizeLargeNumberlatag2nletterconflmoriginLTTltt.coplotltt.linesltt.plotltt.plot.coordsmakeChronosCalibmakeLabelmakeLabel.charactermakeNodeLabelmantel.testmatexpomcconwaysims.testmcmc.popsizemixedFontLabelmltt.plotMoran.IMPRmrcamstmulti2dimulti2di.multiPhylomulti2di.phylomusclemuscle5mvrmvrsNedgeNedge.evonetNedge.multiPhyloNedge.phylonew2old.phylonexus2DNAbinnjnjsNnodeNnode.multiPhyloNnode.phylonode_depthnode_depth_edgelengthnode_heightnode_height_cladonode.depthnode.depth.edgelengthnode.heightnodelabelsnodepathNtipNtip.multiPhyloNtip.phyloold2new.phyloONEwiseparafitpcoaperm.rowscolsphydataplotphylogram.plotphymltestpicpic.orthoplot.evonetplot.multiPhyloplot.phyloplotBreakLongEdgesplotPhyloCoorplotTreeTimepolar2rectpostorderpostprocess.prop.partprint.AAbinprint.DNAbinprint.phyloprop.cladesprop.partrbdtreerbind.DNAbinrcoalrDNAbinread.caicread.dnaread.evonetread.FASTAread.fastqread.GenBankread.gffread.nexusread.nexus.dataread.treereconstructrect2polarreorder.evonetreorder.multiPhyloreorder.phyloreorderRcpprichness.yule.testringrlineagermtopologyrmtreerootroot.multiPhyloroot.phylorotaterotateConstrrphylortopologyrTraitContrTraitDiscrTraitMultrtreerttSDMseg.sitesseq_root2tipSHORTwiseskylineskylineplotskylineplot.deluxeslowinskiguyer.testsolveAmbiguousBasesspeciesTreestreestripLabelsubtreeplotsubtreessummary.phylotcoffeetiplabelstranstreePoptrextriangMtdtriangMtdsultrametricunique.multiPhylounrootunroot.multiPhylounroot.phylounrooted.xyupdateLabelvarcompvarCompPhylipvcvvcv.corPhylvcv.phylovcv2phyloweight.taxoweight.taxo2wherewhich.edgewrite.dnawrite.evonetwrite.FASTAwrite.nexuswrite.nexus.datawrite.treeXplorXplorefilesyuleyule.covyule.timezoom

Dependencies:digestlatticenlmeRcpp

Drawing Phylogenies

Rendered fromDrawingPhylogenies.Rnwusingutils::Sweaveon Aug 21 2024.

Last update: 2024-04-11
Started: 2021-01-04

Moran's I

Rendered fromMoranI.Rnwusingutils::Sweaveon Aug 21 2024.

Last update: 2020-12-28
Started: 2020-12-28

Random Topology

Rendered fromRandomTopologies.Rnwusingutils::Sweaveon Aug 21 2024.

Last update: 2024-03-28
Started: 2020-12-28

Readme and manuals

Help Manual

Help pageTopics
Analyses of Phylogenetics and Evolutionape-package ape
Amino Acid SequencesAAbin AAsubst as.AAbin as.AAbin.AAMultipleAlignment as.AAbin.AAString as.AAbin.AAStringSet as.AAbin.character as.AAbin.list as.character.AAbin as.list.AAbin as.matrix.AAbin as.phyDat.AAbin c.AAbin cbind.AAbin dist.aa image.AAbin labels.AAbin print.AAbin rbind.AAbin [.AAbin
Ancestral Character Estimationace AIC.ace anova.ace deviance.ace logLik.ace print.ace
Add a Scale Bar to a Phylogeny Plotadd.scale.bar
Incomplete Distance Matrix Fillingadditive ultrametric
Alignment Explorer With Multiple Devicesalex
Compare DNA Setsall.equal.DNAbin
Global Comparison of two Phylogeniesall.equal.phylo
Print DNA or AA Sequence Alignementalview
Tools to Explore Filesapetools bydir editFileExtensions Xplor Xplorefiles
Conversion Among DNA Sequence Internal Formatsas.alignment as.character.DNAbin as.DNAbin as.DNAbin.alignment as.DNAbin.character as.DNAbin.DNAMultipleAlignment as.DNAbin.DNAString as.DNAbin.DNAStringSet as.DNAbin.list as.DNAbin.PairwiseAlignmentsSingleSubject
Split Frequencies and Conversion Among Split Classesas.bitsplits as.bitsplits.prop.part as.prop.part as.prop.part.bitsplits bitsplits countBipartitions print.bitsplits sort.bitsplits
Conversion Between Phylo and Matching Objectsas.matching as.matching.phylo as.phylo.matching matching
Conversion Among Tree and Network Objectsas.hclust.phylo as.igraph as.igraph.phylo as.network.phylo as.phylo as.phylo.default as.phylo.hclust as.phylo.phylog new2old.phylo old2new.phylo
Conversion from Taxonomy Variables to Phylogenetic Treesas.phylo.formula
Axis on Side of PhylogenyaxisPhylo
Balance of a Dichotomous Phylogenetic Treebalance
Base frequencies from DNA Sequencesbase.freq Ftab GC.content
Extended Version of the Birth-Death Models to Estimate Speciation and Extinction Ratesbd.ext
Time-Dependent Birth-Death Modelsbd.time
Phylogenetic Generalized Linear Mixed Model for Binary DatabinaryPGLMM binaryPGLMM.sim print.binaryPGLMM
Binds Trees+.phylo bind.tree
Tree Estimation Based on an Improved Version of the NJ Algorithmbionj
Phylogeny of the Families of Birds From Sibley and Ahlquistbird.families
Phylogeny of the Orders of Birds From Sibley and Ahlquistbird.orders
Estimation of Speciation and Extinction Rates With Birth-Death Modelsbirthdeath print.birthdeath
Tree Bipartition and Bootstrapping Phylogeniesboot.phylo plot.prop.part print.prop.part prop.clades prop.part summary.prop.part
Branching Times of a Phylogenetic Treebranching.times
Building Lists of Trees.compressTipLabel .uncompressTipLabel c.multiPhylo c.phylo
Congruence among distance matricesCADM CADM.global CADM.post
Carnivora body sizes and life history traitscarnivora
Check DNA AlignmentscheckAlignment
Checking LabelscheckLabel
Check the Structure of a "phylo" ObjectcheckValidPhylo
Number of Cherries and Null Models of Treescherry
Bat Phylogenychiroptera
Molecular Dating With Mean Path LengthschronoMPL
Molecular Dating With Penalized Likelihoodchronopl
Molecular Dating by Penalised Likelihood and Maximum Likelihoodchronos chronos.control makeChronosCalib print.chronos
Multiple Sequence Alignment with External Applicationsclustal clustalomega efastats letterconf muscle muscle5 tcoffee
Coalescent Intervalscoalescent.intervals coalescent.intervals.default coalescent.intervals.phylo
Collapse Single Nodescollapse.singles has.singles
Collapsed Coalescent Intervalscollapsed.intervals
Cheverud's Comparative Methodcompar.cheverud
Comparative Analysis with GEEscompar.gee drop1.compar.gee predict.compar.gee print.compar.gee
Lynch's Comparative Methodcompar.lynch
Ornstein-Uhlenbeck Model for Continuous Characterscompar.ou
Compare Two "phylo" ObjectscomparePhylo print.comparePhylo
Branch Lengths Computationcompute.brlen
Compute and Set Branching Timescompute.brtime
Concensus Treesconsensus
Pairwise Distances from a Phylogenetic Treecophenetic.phylo dist.nodes
Plots two phylogenetic trees face to face with links between the tips.cophyloplot
Blomberg et al.'s Correlation Structurecoef.corBlomberg corBlomberg corMatrix.corBlomberg
Brownian Correlation Structurecoef.corBrownian corBrownian corMatrix.corBrownian
Phylogenetic Correlation StructurescorClasses corPhyl
Grafen's (1989) Correlation Structurecoef.corGrafen corGrafen corMatrix.corGrafen
Martins's (1997) Correlation Structurecoef.corMartins corMartins corMatrix.corMartins
Pagel's ``lambda'' Correlation Structurecoef.corPagel corMatrix.corPagel corPagel
Correlations among Multiple Traits with Phylogenetic Signalcorphylo print.corphylo
Phylogenetic Correlogramcorrelogram.formula
NEXUS Data Examplecynipids data.nex
Probability Density Under Birth-Death Modelsdbd dbdTime dyule
Definition of Vectors for Plotting or Annotatingdef
Vertex Degrees in Trees and Networksdegree degree.evonet degree.phylo
Delete Alignment Gaps in DNA or AA Sequencesdel.colgapsonly del.gaps del.rowgapsonly
Delta Plotsdelta.plot
Pairwise Distances from DNA Sequencesdist.dna
Pairwise Distances from Genetic Datadist.gene
Topological Distances Between Two Treesdist.topo
Tests of Constant Diversification Ratesdiversi.gof
Analysis of Diversification with Survival Modelsdiversi.time
Diversity Contrast Testdiversity.contrast.test
Manipulate DNA Sequences in Bit-Level Formatas.list.DNAbin as.matrix.DNAbin c.DNAbin cbind.DNAbin DNAbin labels.DNAbin print.DNAbin rbind.DNAbin [.DNAbin
Recode Blocks of IndelsDNAbin2indel
dN/dS Ratiodnds
Remove Tips in a Phylogenetic Treedrop.tip drop.tip.multiPhylo drop.tip.phylo extract.clade keep.tip keep.tip.multiPhylo keep.tip.phylo
Draw Additional Edges on a Plotted Treeedges fancyarrows
Evolutionary Networksas.evonet as.evonet.phylo as.igraph.evonet as.network.evonet as.networx.evonet as.phylo.evonet evonet Nedge.evonet plot.evonet print.evonet read.evonet reorder.evonet write.evonet
Incomplete distances and edge weights of unrooted topologyewLasso
Tree Estimation Based on the Minimum Evolution AlgorithmFastME fastme fastme.bal fastme.ols
Gamma-Statistic of Pybus and HarveygammaStat
Read Annotations from GenBankgetAnnotationsGenBank
Phylogenetic Tree of 193 HIV-1 Sequenceshivtree hivtree.newick hivtree.table
Calculate Numbers of Phylogenetic Treeshowmanytrees LargeNumber print.LargeNumber
Graphical Identification of Nodes and Tipsidentify.phylo
Plot of DNA Sequence Alignementimage.DNAbin
Initialize a `corPhyl' Structure ObjectInitialize.corPhyl
Test for Binary Treeis.binary is.binary.multiPhylo is.binary.phylo is.binary.tree
Check Compatibility of Splitsarecompatible is.compatible is.compatible.bitsplits
Is Group Monophyleticis.monophyletic
Test if a Tree is Ultrametricis.ultrametric is.ultrametric.multiPhylo is.ultrametric.phylo
Plot Multiple Chronograms on the Same Scalekronoviz
Label ManagementabbreviateGenus label2table stripLabel
Ladderize a Treeladderize
Leading and Trailing Alignment Gaps to Nlatag2n
Multiple regression through the originlmorigin lmorigin.ex1 lmorigin.ex2 print.lmorigin
Theoretical Lineage-Through Time PlotsLTT
Lineages Through Time Plotltt.coplot ltt.lines ltt.plot ltt.plot.coords mltt.plot
Label ManagementmakeLabel makeLabel.character makeLabel.DNAbin makeLabel.multiPhylo makeLabel.phylo
Makes Node LabelsmakeNodeLabel makeNodeLabel.multiPhylo makeNodeLabel.phylo
Mantel Test for Similarity of Two Matricesmantel.test
Three Matricesmat3
Five Treesmat5M3ID
Five Independent Treesmat5Mrand
Matrix Exponentialmatexpo
McConway-Sims Test of Homogeneous Diversificationmcconwaysims.test
Reversible Jump MCMC to Infer Demographic Historyextract.popsize lines.popsize mcmc.popsize plot.popsize
Mixed Font Labels for PlottingmixedFontLabel
Moran's I Autocorrelation IndexMoran.I
Most Parsimonious ReconstructionMPR
Find Most Recent Common Ancestors Between PairsgetMRCA mrca
Minimum Spanning Treemst plot.mst
Collapse and Resolve Multichotomiesdi2multi di2multi.multiPhylo di2multi.phylo multi2di multi2di.multiPhylo multi2di.phylo
Manipulating Lists of Trees$.multiPhylo $<-.multiPhylo multiphylo [.multiPhylo [<-.multiPhylo [[.multiPhylo [[<-.multiPhylo
Minimum Variance Reductionmvr mvrs
Neighbor-Joining Tree Estimationnj
Tree Reconstruction from Incomplete Distances With NJ* or bio-NJ*bionjs njs
node.datingestimate.dates estimate.mu node.dating
Depth and Heights of Nodes and Tipsnode.depth node.depth.edgelength node.height
Labelling the Nodes, Tips, and Edges of a Treeedgelabels nodelabels tiplabels
Find Paths of Nodesnodepath
Test of host-parasite coevolutiongopher.D HP.links lice.D parafit print.parafit
Principal Coordinate Analysisbiplot.pcoa pcoa
Tree Annotationphydataplot ring
Fits a Bunch of Models with PhyMLphymltest plot.phymltest print.phymltest summary.phymltest
Phylogenetically Independent Contrastspic
Phylogenetically Independent Orthonormal Contrastspic.ortho
Plot a Correlogramplot.correlogram plot.correlogramList
Plot Phylogeniesplot.multiPhylo plot.phylo
Extra Fuctions to Plot and Annotate PhylogeniesdrawSupportOnEdges plot.phylo.extra plotBreakLongEdges
Plot Variance Componentsplot.varcomp
Plot Tree With Time AxisplotTreeTime
Compact Display of a Phylogenyprint.multiPhylo print.phylo str.multiPhylo
Random DNA SequencesrDNAbin
Read Tree File in CAIC Formatread.caic
Read DNA Sequences in a Fileread.dna read.FASTA read.fastq
Read DNA Sequences from GenBank via Internetread.GenBank
Read GFF Filesread.gff
Read Tree File in Nexus Formatread.nexus
Read Character Data In NEXUS Formatnexus2DNAbin read.nexus.data
Read Tree File in Parenthetic Formatphylo read.tree
Continuous Ancestral Character Estimationreconstruct
Internal Reordering of Treescladewise postorder reorder.multiPhylo reorder.phylo
Test of Diversification-Shift With the Yule Processrichness.yule.test
Tree Simulation Under the Time-Dependent Birth-Death Modelsdrop.fossil rbdtree rlineage rphylo
Roots Phylogenetic Treesis.rooted is.rooted.multiPhylo is.rooted.phylo root root.multiPhylo root.phylo unroot unroot.multiPhylo unroot.phylo
Swapping Sister Cladesrotate rotateConstr
Continuous Character SimulationrTraitCont
Discrete Character SimulationrTraitDisc
Multivariate Character SimulationrTraitMult
Generate Random Treesrcoal rmtopology rmtree rtopology rtree
Root a Tree by Root-to-Tip Regressionrtt
Construction of Consensus Distance Matrix With SDMSDM
Find Segregating Sites in DNA Sequencesseg.sites
Skyline Plot Estimate of Effective Population Sizefind.skyline.epsilon skyline skyline.coalescentIntervals skyline.collapsedIntervals skyline.phylo
Drawing Skyline Plot Graphslines.skyline plot.skyline skylineplot skylineplot.deluxe
Slowinski-Guyer Test of Homogeneous Diversificationslowinskiguyer.test
Solve Ambiguous Bases in DNA SequencessolveAmbiguousBases
Species Tree EstimationspeciesTree
Generates Systematic Regular Treesstree
Zoom on a Portion of a Phylogeny by Successive Clickssubtreeplot
All subtrees of a Phylogenetic Treesubtrees
Print Summary of a PhylogenyNedge Nedge.multiPhylo Nedge.phylo Nnode Nnode.multiPhylo Nnode.phylo Ntip Ntip.multiPhylo Ntip.phylo summary.phylo
Translation from DNA to Amino Acid Sequencescomplement trans
Tree PoppingtreePop
Tree Explorer With Multiple Devicestrex
Tree Reconstruction Based on the Triangles MethodtriangMtd triangMtds
Revomes Duplicate Treesunique.multiPhylo
Update LabelsupdateLabel updateLabel.AAbin updateLabel.character updateLabel.data.frame updateLabel.DNAbin updateLabel.evonet updateLabel.matrix updateLabel.phylo
Compute Variance Component Estimatesvarcomp
Variance Components with Orthonormal ContrastsvarCompPhylip
Phylogenetic Variance-covariance or Correlation Matrixvcv vcv.corPhyl vcv.phylo
Variance-Covariance Matrix to Treevcv2phylo
Define Similarity Matrixweight.taxo weight.taxo2
Find Patterns in DNA Sequenceswhere
Identifies Edges of a Treewhich.edge
Cytochrome b Gene Sequences of Woodmicewoodmouse
Write DNA Sequences in a Filewrite.dna write.FASTA
Write Tree File in Nexus Formatwrite.nexus
Write Character Data in NEXUS Formatwrite.nexus.data
Write Tree File in Parenthetic Formatwrite.tree
Fits the Yule Model to a Phylogenetic Treeyule
Fits the Yule Model With Covariatesyule.cov
Fits the Time-Dependent Yule Modelyule.time
Zoom on a Portion of a Phylogenyzoom