Dtest                   Conducts correlational D-test from stochastic
                        mapping
add.arrow               Add an arrow pointing to a tip or node on the
                        tree
add.color.bar           Add color bar to a plot
add.everywhere          Add tip to all edges in a tree
add.random              Add tips at random to the tree
add.simmap.legend       Add legend to stochastically mapped tree
add.species.to.genus    Add species to genus on a phylogeny or bind
                        simulated species subtrees to a backbone genus
                        tree
aic.w                   Computes Akaike weights
allFurcTrees            Generate all bi- and multifurcating unrooted
                        trees
anc.Bayes               Bayesian ancestral character estimation
anc.ML                  Ancestral character estimation using likelihood
anc.trend               Ancestral character estimation with a trend
ancThresh               Ancestral character estimation under the
                        threshold model using Bayesian MCMC
ancr                    Compute marginal or joint ancestral state
                        estimates
anoletree               Phylogenetic datasets
ansi_phylo              Graph a phylogeny using only ANSI characters
applyBranchLengths      Applies the branch lengths of a reference tree
                        to a target
as.Qmatrix              Convert a fitted M_k_ model to a Q-matrix
as.multiPhylo           Conversion to object of class '"multiPhylo"'
ave.rates               Average the posterior rates
averageTree             Compute an average tree from a set of trees and
                        related operations
bd                      Convert object of class '"birthdeath"' to raw
                        birth & death rates
bind.tip                Attaches a new tip to a tree
bind.tree.simmap        Binds two trees of class '"simmap"'
bmPlot                  Simulates and visualizes continuous trait
                        evolution on a phylogeny
bounded_bm              Fits bounded and wrapped Brownian motion models
branching.diffusion     Animation of branching random diffusion
brownie.lite            Likelihood test for rate variation in a
                        continuous trait
brownieREML             REML version of 'brownie.lite'
cladelabels             Add labels to subtrees of a plotted phylogeny
collapse.to.star        Collapse a subtree to a star phylogeny
collapseTree            Interactive tree visualizer
compare.chronograms     Compares two chronograms with precisely
                        matching nodes in a visual manner
consensus.edges         Compute consensus edges for a tree under some
                        criterion
contMap                 Map continuous trait evolution on the tree
cophylo                 Creates a co-phylogenetic plot
cospeciation            Conducts a statistical test of cospeciation
                        between two trees
countSimmap             Counts the number of character changes on a
                        object of class '"simmap"' or '"multiSimmap"'
ctt                     Generates (or simulates) a 'changes through
                        time' plot from a set of stochastic map
                        character histories
density.multiSimmap     Computes a posterior distribution for the
                        number and types of changes on the tree
densityMap              Plot posterior density of stochastic mapping on
                        a tree
densityTree             Plots a posterior sample of trees
describe.simmap         Summarizes a stochastic mapped tree or set of
                        trees
di2multi.simmap         Collapse or resolve polytomies in a tree with a
                        character painted on the edges
dotTree                 Creates a phylogenetic dot plot
drop.clade              Drop a clade from a tree
drop.leaves             Drop all the leaves (tips) from a tree
drop.tip.contMap        Drop tip or tips from an object of class
                        '"contMap"' or '"densityMap"'
drop.tip.multiSimmap    Drop or keep tip or tips from an object of
                        class '"multiSimmap"'
drop.tip.simmap         Drop tips or extract clade from tree with
                        mapped discrete character
edge.widthMap           Map continuous trait evolution on the tree
edgeProbs               Compute the relative frequencies of state
                        changes along edges
estDiversity            Estimate diversity at each node of the tree
evol.rate.mcmc          Bayesian MCMC method for identifying
                        exceptional phenotypic diversification in a
                        phylogeny
evol.vcv                Likelihood test for variation in the
                        evolutionary variance-covariance matrix
evolvcv.lite            Likelihood test for a shift in the evolutionary
                        correlation between traits
exhaustiveMP            Exhaustive and branch & bound MP optimization
expand.clade            Expands (or contracts) the tip-spacing of a
                        given clade or clades
export.as.xml           Export trees & data in XML format
fancyTree               Plots special types of phylogenetic trees
fastAnc                 (Reasonably) fast estimation of ML ancestral
                        states
fastBM                  (Reasonably) fast quantitative trait simulation
                        on phylogenies
fastMRCA                Get the MRCA (or height above the root of the
                        MRCA) of a pair of tip taxa
findMRCA                Get the MRCA of a set of taxa
fit.bd                  Fits birth-death (speciation/extinction) model
                        to reconstructed phylogeny
fitBayes                Evolutionary model fitting with intraspecific
                        variability using Bayesian MCMC
fitDiversityModel       Fit diversity-dependent phenotypic evolution
                        model
fitMk                   Fits extended M_k_ model for discrete character
                        evolution
fitPagel                Function to test for correlated evolution of
                        binary traits
fitThresh               Fits binary, multi-state, and semi-threshold
                        models using the discretized diffusion
                        approximation
fitcontMk               Fits binary discrete character evolution model
                        where the transition rate varies as a function
                        of a continuous trait
fitmultiBM              Fits multi-rate (or multi-trend) discrete
                        character dependent continuous trait evolution
force.ultrametric       Coerces a phylogenetic tree to be ultrametric
gamma_pruning           Internally used function
gammatest               gamma test of Pybus & Harvey (2000)
genSeq                  Simulate a DNA alignment on the tree under a
                        model
geo.legend              Adds a geological (or other temporal) legend to
                        a plotted tree
get.treepos             Get position or node of a plotted tree
                        interactively
getCladesofSize         Get all subtrees larger than or equal to a
                        specified size
getDescendants          Get descendant node numbers
getExtant               Returns a list of the extant or extinct
                        lineages in a tree containing
                        non-contemporaneous tips
getSisters              Get the sister node number, label, or set of
                        nodes for a node or tip
getStates               Get the states at nodes or tips from a mapped
                        tree
labelnodes              Function to interactively label nodes of a
                        plotted tree
ladderize.simmap        Ladderize a tree with a mapped discrete
                        character
lambda.transform        lambda transformation of matrix
likMlambda              Likelihood for joint lambda
linklabels              Function to add tip labels to a plotted tree
                        with linking lines
locate.fossil           Locate a fossil lineage in a tree using
                        continuous characters
locate.yeti             Locate a cryptic, recently extinct, or missing
                        taxon on a tree
ls.tree                 Least squares branch lengths for a given tree
ltt                     Creates lineage-through-time plot (including
                        extinct lineages)
ltt95                   Creates a (1-alpha)% CI for a set of LTTs
make.era.map            Create "era" map on a phylogenetic tree
make.simmap             Simulate stochastic character maps on a
                        phylogenetic tree or trees
map.overlap             Proportional overlap between two mapped
                        character histories on a tree
map.to.singleton        Converts a tree without singletons to a tree
                        with singleton nodes
mapped.states           Returns a vector, matrix, or list of the mapped
                        states on a tree or set of trees
markChanges             Add marked changes to a plotted tree with
                        mapped discrete character
matchNodes              Matches nodes between two trees
mergeMappedStates       Merge two or more mapped states into one state
midpoint_root           Midpoint root a phylogeny
minRotate               Rotates all nodes of the tree to minimize the
                        difference in order with a vector
minSplit                Finding the minimum (median) split in the
                        posterior sample
modified.Grafen         Computes modified Grafen edge lengths
mrp.supertree           Matrix representation parsimony supertree
                        estimation
multi.mantel            Multiple matrix regression (partial Mantel
                        test)
multiC                  Returns a list with phylogenetic VCV matrix for
                        each mapped state
multiRF                 Computes Robinson-Foulds distance between a set
                        of trees
multirateBM             Function to fit a multi-rate Brownian evolution
                        model
nodeHeights             Compute the heights above the root of each node
nodelabels.cophylo      Add labels to a plotted "cophylo" object
optim.phylo.ls          Phylogeny inference using the least squares
                        method
orderMappedEdge         Order the columns of 'mapped.edge' to match
                        across trees
paintSubTree            Paint sub-trees with a discrete character
paste.tree              Paste two trees together
pbtree                  Simulate pure-birth or birth-death stochastic
                        tree or trees
pgls.Ives               Phylogenetic regression with intraspecific
                        sampling error
phenogram               Plot traitgram (phenogram)
phyl.RMA                Phylogenetic reduced major axis (RMA)
                        regression
phyl.cca                Phylogenetic canonical correlation analysis
phyl.pairedttest        Phylogenetic paired _t_-test
phyl.pca                Phylogenetic principal components analysis
phyl.resid              Phylogenetic size-correction via GLS regression
phyl.vcv                Compute evolutionary VCV matrix for a tree &
                        dataset
phylANOVA               Phylogenetic ANOVA and post-hoc tests
phylo.heatmap           Creates a phylogenetic heat map
phylo.impute            Phylogenetic imputation for multivariate
                        continuous character data
phylo.to.map            Plot tree with tips linked to geographic
                        coordinates
phylo.toBackbone        Converts tree to backbone or vice versa
phyloDesign             Compute design matrix for least squares
                        analyses
phylomorphospace        Creates phylomorphospace plot
phylomorphospace3d      Creates three-dimensional phylomorphospace plot
phylosig                Compute phylogenetic signal with two methods
phytools-package        phytools: Phylogenetic Tools for comparative
                        biology (and other things)
plot.backbonePhylo      Plots backbone tree with triangles as clades
plotBranchbyTrait       Plot branch colors by a quantitative trait or
                        value
plotSimmap              Plot stochastic character mapped tree
plotThresh              Tree plotting with posterior probabilities of
                        ancestral states from the threshold model
plotTree                Plots rooted phylogenetic tree
plotTree.datamatrix     Plot a tree with a discrete (or continuous)
                        character data matrix at the tips
plotTree.errorbars      Plot a tree with error bars around divergence
                        dates
plotTree.lollipop       Plot a tree with one or more matched lollipop
                        plots
plotTree.wBars          Plot a tree with bars at the tips
posterior.evolrate      Analysis of the posterior sample from
                        evol.rate.mcmc
posthoc                 Generic post-hoc test
print.backbonePhylo     Print method for backbone phylogeny
pscore                  Compute the parsimony score
ratebystate             Method for investigating the rate of one trait
                        as a function of the state of another
ratebytree              Likelihood test for rate variation among trees,
                        clades, or traits
rateshift               Find the temporal position of one or more rate
                        shifts
read.newick             Newick or Nexus style tree reader
read.simmap             Read SIMMAP style trees from file
reorder.backbonePhylo   Reorders a backbone phylogeny
reorderSimmap           Reorder edges of a '"simmap"' tree
rep.phylo               Replicate a tree or set of trees
reroot                  Re-root a tree along an edge
rerootingMethod         Get marginal ancestral state reconstructions by
                        re-rooting
rescale                 Rescale phylogenetic objects of different types
rescale.simmap          Rescale object of class '"simmap"'
resolveNode             Compute all possible resolutions of a node or
                        all nodes in a multifurcating tree
rotateNodes             Rotates a node or set of nodes in a
                        phylogenetic tree
roundBranches           Rounds the branch lengths of a tree
roundPhylogram          Plot a round, sigmoidal, or spline phylogram or
                        cladogram
rstate                  Pick a random state according to a vector of
                        probabilities
sampleFrom              Sample from a set of distributions
setMap                  Set color map for various phylogenetic objects
                        of classes
sim.corrs               Multivariate Brownian simulation with multiple
                        correlations and rates
sim.history             Simulate character history or a discrete
                        character at the tips of the tree under some
                        model
sim.ratebystate         Conduct simulation of state dependent rate
                        variation
sim.rates               Brownian or OU simulation with multiple
                        evolutionary regimes
simBMphylo              Creates a graphical illustration of Brownian
                        motion evolution on a phylogeny
skewers                 Matrix comparison using the method of random
                        skewers
splitEdgeColor          Split edge colors when descendant edges have
                        different mapped states
splitTree               Split tree at a point
splitplotTree           Plots a phylogeny in two columns
starTree                Create star phylogeny
strahlerNumber          Computes Strahler number for trees and nodes
threshBayes             Threshold model using Bayesian MCMC
threshDIC               Deviance Information Criterion from the
                        threshold model
threshState             Computes value for a threshold character from a
                        liability and thresholds
to.matrix               Convert a character vector to a binary matrix
tree.grow               Creates an animation of a tree growing from
                        left-to-right or upwards
treeSlice               Slices the tree at a particular point and
                        returns all subtrees, or the tree rootward of
                        the point
untangle                Attempts to untangle crossing branches for
                        plotting
vcvPhylo                Calculates cophenetic (i.e., phylogenetic VCV)
                        matrix
write.simmap            Write a stochastic character mapped tree to
                        file
writeAncestors          Write a tree to file with ancestral states and
                        (optionally) CIs at nodes
writeNexus              Write a tree to file in Nexus format
