Man pages for phytools
Phylogenetic Tools for Comparative Biology (and Other Things)

add.arrowAdd an arrow pointing to a tip or node on the tree
add.color.barAdd color bar to a plot
add.everywhereAdd tip to all edges in a tree
add.randomAdd tips at random to the tree
add.simmap.legendAdd legend to stochastically mapped tree
add.species.to.genusAdd species to genus on a phylogeny or bind simulated species...
aic.wComputes AIC weights
allFurcTreesGenerate all bi- and multifurcating unrooted trees
anc.BayesBayesian ancestral character estimation
anc.MLAncestral character estimation using likelihood
ancThreshAncestral character estimation under the threshold model...
anc.trendAncestral character estimation with a trend
anoletreePhylogenetic datasets
applyBranchLengthsApplies the branch lengths of a reference tree to a target
as.multiPhyloConversion to object of class '"multiPhylo"'
as.QmatrixConvert a fitted M_k_ model to a Q-matrix
averageTreeCompute an average tree from a set of trees and related...
ave.ratesAverage the posterior rates
bdConvert object of class "birthdeath" to raw birth & death...
bind.tipAttaches a new tip to a tree
bind.tree.simmapAttaches a new tip to a tree
bmPlotSimulates and visualizes discrete-time Brownian evolution on...
branching.diffusionAnimation of branching random diffusion
brownie.liteLikelihood test for rate variation in a continuous trait
brownieREMLREML version of brownie.lite
cladelabelsAdd labels to subtrees of a plotted phylogeny
collapse.to.starCollapse a subtree to a star phylogeny
collapseTreeInteractive tree visualizer
compare.chronogramsCompares two chronograms with precisely matching nodes in a...
consensus.edgesCompute consensus edges for a tree under some criterion
contMapMap continuous trait evolution on the tree
cophyloCreates a co-phylogenetic plot
cospeciationConducts a statistical test of cospeciation between two trees
countSimmapCounts the number of character changes on a object of class...
cttGenerates (or simulates) a 'changes through time' plot from a...
densityMapPlot posterior density of stochastic mapping on a tree
density.multiSimmapComputes a posterior distribution for the number and types of...
densityTreePlots a posterior sample of trees
describe.simmapSummarizes a stochastic mapped tree or set of trees
di2multi.simmapCollapse or resolve polytomies in a tree with a character...
dotTreeCreates a phylogenetic dot plot
drop.cladeDrop a clade from a tree
drop.leavesDrop all the leaves (tips) from a tree
drop.tip.contMapDrop tip or tips from an object of class "contMap" or...
drop.tip.multiPhyloDrop tip or tips from an object of class "multiPhylo" or...
drop.tip.simmapDrop tips or extract clade from tree with mapped discrete...
DtestConducts correlational D-test from stochastic mapping
edgeProbsCompute the relative frequencies of state changes along edges
edge.widthMapMap continuous trait evolution on the tree
estDiversityEstimate diversity at each node of the tree
evol.rate.mcmcBayesian MCMC method for identifying exceptional phenotypic...
evol.vcvLikelihood test for variation in the evolutionary...
evolvcv.liteLikelihood test for a shift in the evolutionary correlation...
exhaustiveMPExhaustive and branch & bound MP optimization
expand.cladeExpands (or contracts) the tip-spacing of a given clade or...
export.as.xmlExport trees & data in XML format
fancyTreePlots special types of phylogenetic trees
fastAnc(Reasonably) fast estimation of ML ancestral states
fastBM(Reasonably) fast quantitative trait simulation on...
fastMRCAGet the MRCA (or height above the root of the MRCA) of a pair...
findMRCAGet the MRCA of a set of taxa
fitBayesEvolutionary model fitting with intraspecific variability...
fit.bdFits birth-death (speciation/extinction) model to...
fitDiversityModelFit diversity-dependent phenotypic evolution model
fitMkFits Mk model
fitPagelFunction to test for correlated evolution of binary traits
force.ultrametricForces a phylogenetic tree to be ultrametric
gammatestGamma test of Pybus & Harvey (2000)
genSeqSimulate a DNA alignment on the tree under a model
geo.legendAdds a geological (or other temporal) legend to a plotted...
getCladesofSizeGet all subtrees larger than or equal to a specified size
getDescendantsGet descendant node numbers
getExtantReturns a list of the extant or extinct lineages in a tree...
getSistersGet the sister node number, label, or set of nodes for a node...
getStatesGet the states at nodes or tips from a mapped tree
get.treeposGet position or node of a plotted tree interactively
labelnodesFunction to interactively label nodes of a plotted tree
ladderize.simmapLadderize a tree with a mapped discrete character
lambda.transformlambda transformation of matrix
likMlambdaLikelihood for joint lambda
linklabelsFunction to add tip labels to a plotted tree with linking...
locate.fossilLocate a fossil lineage in a tree using continuous characters
locate.yetiLocate a cryptic, recently extinct, or missing taxon on a...
ls.treeLeast squares branch lengths for a given tree
lttCreates lineage-through-time plot (including extinct...
ltt95Creates a (1-alpha)-percent CI for a set of LTTs
make.era.mapCreate "era" map on a phylogenetic tree
make.simmapSimulate stochastic character maps on a phylogenetic tree or...
map.overlapProportional overlap between two mapped character histories...
mapped.statesReturns a vector, matrix, or list of the mapped states on a...
map.to.singletonConverts a tree without singletons to a tree with singleton...
markChangesAdd marked changes to a plotted tree with mapped discrete...
matchNodesMatches nodes between two trees
mergeMappedStatesMerge two or more mapped states into one state
midpoint.rootMidpoint root a phylogeny
minRotateRotates all nodes of the tree to minimize the difference in...
minSplitFinding the minimum (median) split in the posterior sample
modified.GrafenComputes modified Grafen edge lengths
mrp.supertreeMatrix representation parsimony supertree estimation
multiCReturns a list with phylogenetic VCV matrix for each mapped...
multi.mantelMultiple matrix regression (partial Mantel test)
multirateBMFunction to fit a multi-rate Brownian evolution model
multiRFComputes Robinson-Foulds distance between a set of trees
nodeHeightsCompute the heights above the root of each node
nodelabels.cophyloAdd labels to a plotted "cophylo" object
optim.phylo.lsPhylogeny inference using the least squares method
orderMappedEdgeOrder the columns of mapped.edge to match across trees
paintSubTreePaint sub-trees with a discrete character
paste.treePaste two trees together
pbtreeSimulate pure-birth or birth-death stochastic tree or trees
pgls.IvesPhylogenetic regression with intraspecific sampling error
phenogramPlot phenogram (traitgram)
phylANOVAPhylogenetic ANOVA and post-hoc tests
phyl.ccaPhylogenetic canonical correlation analysis
phyloDesignCompute design matrix for least squares analyses
phylo.heatmapCreates a phylogenetic heat map
phylo.imputePhylogenetic imputation for multivariate continuous character...
phylomorphospaceCreates phylomorphospace plot
phylomorphospace3dCreates tree-dimensional phylomorphospace plot
phylosigCompute phylogenetic signal with two methods
phylo.toBackboneConverts tree to backbone or vice versa
phylo.to.mapPlot tree with tips linked to geographic coordinates
phyl.pairedttestPhylogenetic paired t-test
phyl.pcaPhylogenetic principal components analysis
phyl.residPhylogenetic size-correction via GLS regression
phyl.RMAPhylogenetic reduced major axis (RMA) regression
phyl.vcvCompute evolutionary VCV matrix for a tree & dataset
phytools-packagephytools: Phylogenetic Tools for comparative biology (and...
plot.backbonePhyloPlots backbone tree with triangles as clades
plotBranchbyTraitPlot branch colors by a quantitative trait or value
plotSimmapPlot stochastic character mapped tree
plotThreshTree plotting with posterior probabilities of ancestral...
plotTreePlots rooted phylogenetic tree
plotTree.datamatrixPlot a tree with a discrete character data matrix at the tips
plotTree.errorbarsPlot a tree with error bars around divergence dates
plotTree.wBarsPlot a tree with bars at the tips
posterior.evolrateAnalysis of the posterior sample from evol.rate.mcmc
posthocGeneric post-hoc test
print.backbonePhyloPrint method for backbone phylogeny
ratebystateMethod for investigating the rate of one trait as a function...
ratebytreeLikelihood test for rate variation among trees, clades, or...
rateshiftFind the temporal position of one or more rate shifts
read.newickNewick or Nexus style tree reader
read.simmapRead SIMMAP style trees from file
reorder.backbonePhyloReorders a backbone phylogeny
reorderSimmapReorder edges of a simmap tree
rep.phyloReplicate a tree or set of trees
rerootRe-root a tree along an edge
rerootingMethodGet marginal ancestral state reconstructions by re-rooting
rescaleSimmapRescale SIMMAP style tree
resolveNodeCompute all possible resolutions of a node or all nodes in a...
rotateNodesRotates a node or set of nodes in a phylogenetic tree
roundBranchesRounds the branch lengths of a tree
roundPhylogramPlot a round or sigmoidal phylogram or cladogram
rstatePick a random state according to a vector of probabilities
sampleFromSample from a set of distributions
setMapSet color map for various phylogenetic objects of classes
simBMphyloCreates a graphical illustration of Brownian motion evolution...
sim.corrsMultivariate Brownian simulation with multiple correlations...
sim.historySimulate character history or a discrete character at the...
sim.ratebystateConduct simulation of state dependent rate variation
sim.ratesBrownian or OU simulation with multiple evolutionary regimes
skewersMatrix comparison using the method of random skewers
splitEdgeColorSplit edge colors when descendant edges have different mapped...
splitplotTreePlots a phylogeny in two columns
splitTreeSplit tree at a point
starTreeCreate star phylogeny
strahlerNumberComputes Strahler number for trees and nodes
threshBayesThreshold model using Bayesian MCMC
threshDICDeviance Information Criterion from the threshold model
threshStateComputes value for a threshold character from a liability and...
to.matrixConvert a character vector to a binary matrix
tree.growCreates an animation of a tree growing from left-to-right or...
treeSliceSlices the tree at a particular point and returns all...
untangleAttempts to untangle crossing branches for plotting
vcvPhyloCalculates cophenetic (i.e., phylogenetic VCV) matrix
writeAncestorsWrite a tree to file with ancestral states and (optionally)...
writeNexusWrite a tree to file in Nexus format
write.simmapWrite a stochastic character mapped tree to file
phytools documentation built on Sept. 2, 2022, 1:06 a.m.