Man pages for ape
Analyses of Phylogenetics and Evolution

AAbinAmino Acid Sequences
aceAncestral Character Estimation
additiveIncomplete Distance Matrix Filling
add.scale.barAdd a Scale Bar to a Phylogeny Plot
alexAlignment Explorer With Multiple Devices
all.equal.DNAbinCompare DNA Sets
all.equal.phyloGlobal Comparison of two Phylogenies
alviewPrint DNA or AA Sequence Alignement
ape-internalInternal Ape Functions
ape-packageAnalyses of Phylogenetics and Evolution
apetoolsTools to Explore Files
as.alignmentConversion Among DNA Sequence Internal Formats
as.bitsplitsSplit Frequencies and Conversion Among Split Classes
as.matchingConversion Between Phylo and Matching Objects
as.phyloConversion Among Tree and Network Objects
as.phylo.formulaConversion from Taxonomy Variables to Phylogenetic Trees
axisPhyloAxis on Side of Phylogeny
balanceBalance of a Dichotomous Phylogenetic Tree
base.freqBase frequencies from DNA Sequences
bd.extExtended Version of the Birth-Death Models to Estimate...
bd.timeTime-Dependent Birth-Death Models
binaryPGLMMPhylogenetic Generalized Linear Mixed Model for Binary Data
bind.treeBinds Trees
bionjTree Estimation Based on an Improved Version of the NJ...
bird.familiesPhylogeny of the Families of Birds From Sibley and Ahlquist
bird.ordersPhylogeny of the Orders of Birds From Sibley and Ahlquist
birthdeathEstimation of Speciation and Extinction Rates With...
boot.phyloTree Bipartition and Bootstrapping Phylogenies
branching.timesBranching Times of a Phylogenetic Tree
CADM.globalCongruence among distance matrices
carnivoraCarnivora body sizes and life history traits
checkAlignmentCheck DNA Alignments
checkLabelChecking Labels
checkValidPhyloCheck the Structure of a "phylo" Object
cherryNumber of Cherries and Null Models of Trees
chiropteraBat Phylogeny
chronoMPLMolecular Dating With Mean Path Lengths
chronoplMolecular Dating With Penalized Likelihood
chronosMolecular Dating by Penalised Likelihood and Maximum...
clustalMultiple Sequence Alignment with External Applications
coalescent.intervalsCoalescent Intervals
collapsed.intervalsCollapsed Coalescent Intervals
collapse.singlesCollapse Single Nodes
compar.cheverudCheverud's Comparative Method
comparePhyloCompare Two "phylo" Objects
compar.geeComparative Analysis with GEEs
compar.lynchLynch's Comparative Method
compar.ouOrnstein-Uhlenbeck Model for Continuous Characters
compute.brlenBranch Lengths Computation
compute.brtimeCompute and Set Branching Times
consensusConcensus Trees
cophenetic.phyloPairwise Distances from a Phylogenetic Tree
cophyloplotPlots two phylogenetic trees face to face with links between...
corBlombergBlomberg et al.'s Correlation Structure
corBrownianBrownian Correlation Structure
corClassesPhylogenetic Correlation Structures
corGrafenGrafen's (1989) Correlation Structure
corMartinsMartins's (1997) Correlation Structure
corPagelPagel's "lambda" Correlation Structure
corphyloCorrelations among Multiple Traits with Phylogenetic Signal
correlogram.formulaPhylogenetic Correlogram
c.phyloBuilding Lists of Trees
cynipidsNEXUS Data Example
dbdProbability Density Under Birth-Death Models
defDefinition of Vectors for Plotting or Annotating
degreeVertex Degrees in Trees and Networks
del.gapsDelete Alignment Gaps in DNA Sequences
delta.plotDelta Plots
dist.dnaPairwise Distances from DNA Sequences
dist.genePairwise Distances from Genetic Data
dist.topoTopological Distances Between Two Trees
diversi.gofTests of Constant Diversification Rates
diversi.timeAnalysis of Diversification with Survival Models
diversity.contrast.testDiversity Contrast Test
DNAbinManipulate DNA Sequences in Bit-Level Format
DNAbin2indelRecode Blocks of Indels
dndsdN/dS Ratio
drop.tipRemove Tips in a Phylogenetic Tree
edgesDraw Additional Edges on a Plotted Tree
evonetEvolutionary Networks
ewLassoIncomplete distances and edge weights of unrooted topology
fastmeTree Estimation Based on the Minimum Evolution Algorithm
gammaStatGamma-Statistic of Pybus and Harvey
getAnnotationsGenBankRead Annotations from GenBank
hivtreePhylogenetic Tree of 193 HIV-1 Sequences
howmanytreesCalculate Numbers of Phylogenetic Trees
identify.phyloGraphical Identification of Nodes and Tips
image.DNAbinPlot of DNA Sequence Alignement
Initialize.corPhylInitialize a 'corPhyl' Structure Object
is.binary.treeTest for Binary Tree
is.compatibleCheck Compatibility of Splits
is.monophyleticIs Group Monophyletic
is.ultrametricTest if a Tree is Ultrametric
kronovizPlot Multiple Chronograms on the Same Scale
label2tableLabel Management
ladderizeLadderize a Tree
latag2nLeading and Trailing Alignment Gaps to N
lmoriginMultiple regression through the origin
LTTTheoretical Lineage-Through Time Plots
ltt.plotLineages Through Time Plot
makeLabelLabel Management
makeNodeLabelMakes Node Labels
mantel.testMantel Test for Similarity of Two Matrices
mat3Three Matrices
mat5M3IDFive Trees
mat5MrandFive Independent Trees
matexpoMatrix Exponential
mcconwaysims.testMcConway-Sims Test of Homogeneous Diversification
mcmc.popsizeReversible Jump MCMC to Infer Demographic History
mixedFontLabelMixed Font Labels for Plotting
MoranIMoran's I Autocorrelation Index
MPRMost Parsimonious Reconstruction
mrcaFind Most Recent Common Ancestors Between Pairs
mstMinimum Spanning Tree
multi2diCollapse and Resolve Multichotomies
multiphyloManipulating Lists of Trees
mvrMinimum Variance Reduction
njNeighbor-Joining Tree Estimation
njsTree Reconstruction from Incomplete Distances With NJ* or...
node.depthDepth and Heights of Nodes and Tips
nodelabelsLabelling the Nodes, Tips, and Edges of a Tree
nodepathFind Paths of Nodes
parafitTest of host-parasite coevolution
pcoaPrincipal Coordinate Analysis
phydataplotTree Annotation
phymltestFits a Bunch of Models with PhyML
picPhylogenetically Independent Contrasts
pic.orthoPhylogenetically Independent Orthonormal Contrasts
plot.correlogramPlot a Correlogram
plot.phyloPlot Phylogenies
plot.phyloExtraExtra Fuctions to Plot and Annotate Phylogenies
plotTreeTimePlot Tree With Time Axis
plot.varcompPlot Variance Components
print.phyloCompact Display of a Phylogeny
rDNAbinRandom DNA Sequences
read.caicRead Tree File in CAIC Format
read.dnaRead DNA Sequences in a File
read.GenBankRead DNA Sequences from GenBank via Internet
read.gffRead GFF Files
read.nexusRead Tree File in Nexus Format Character Data In NEXUS Format
read.treeRead Tree File in Parenthetic Format
reconstructContinuous Ancestral Character Estimation
reorder.phyloInternal Reordering of Trees
richness.yule.testTest of Diversification-Shift With the Yule Process
rlineageTree Simulation Under the Time-Dependent Birth-Death Models
rootRoots Phylogenetic Trees
rotateSwapping Sister Clades
rTraitContContinuous Character Simulation
rTraitDiscDiscrete Character Simulation
rTraitMultMultivariate Character Simulation
rtreeGenerate Random Trees
rttRoot a Tree by Root-to-Tip Regression
SDMConstruction of Consensus Distance Matrix With SDM
seg.sitesFind Segregating Sites in DNA Sequences
skylineSkyline Plot Estimate of Effective Population Size
skylineplotDrawing Skyline Plot Graphs
slowinskiguyer.testSlowinski-Guyer Test of Homogeneous Diversification
solveAmbiguousBasesSolve Ambiguous Bases in DNA Sequences
speciesTreeSpecies Tree Estimation
streeGenerates Systematic Regular Trees
subtreeplotZoom on a Portion of a Phylogeny by Successive Clicks
subtreesAll subtrees of a Phylogenetic Tree
summary.phyloPrint Summary of a Phylogeny
transTranslation from DNA to Amino Acid Sequences
treePopTree Popping
trexTree Explorer With Multiple Devices
triangMtdTree Reconstruction Based on the Triangles Method
unique.multiPhyloRevomes Duplicate Trees
updateLabelUpdate Labels
varcompCompute Variance Component Estimates
varCompPhylipVariance Components with Orthonormal Contrasts
vcv2phyloVariance-Covariance Matrix to Tree
vcv.phyloPhylogenetic Variance-covariance or Correlation Matrix
weight.taxoDefine Similarity Matrix
whereFind Patterns in DNA Sequences
which.edgeIdentifies Edges of a Tree
woodmouseCytochrome b Gene Sequences of Woodmice
write.dnaWrite DNA Sequences in a File
write.nexusWrite Tree File in Nexus Format Character Data in NEXUS Format
write.treeWrite Tree File in Parenthetic Format
yuleFits the Yule Model to a Phylogenetic Tree
yule.covFits the Yule Model With Covariates
yule.timeFits the Time-Dependent Yule Model
zoomZoom on a Portion of a Phylogeny
ape documentation built on March 31, 2023, 6:56 p.m.