Ancestral character estimation using likelihood
Compares two chronograms with precisely matching nodes in a visual manner
Compute consensus edges for a tree under some criterion
Conversion to object of class "multiPhylo"
Map continuous trait evolution on the tree
Creates a phylogenetic dot plot
Evolutionary model fitting with intraspecific variability using Bayesian MCMC
Fits birth-death (speciation/extinction) model to reconstructed phylogeny
Ancestral character estimation with a trend
Bayesian ancestral character estimation
Creates a co-phylogenetic plot
Ancestral character estimation under the threshold model using Bayesian MCMC
Convert object of class "birthdeath" to raw birth & death rates
Phylogeny of Greater Antillean anole ecomorph species with mapped discrete character
Attaches a new tip to a tree
REML version of brownie.lite
Average the posterior rates
Applies the branch lengths of a reference tree to a target
Drop a clade from a tree
Collapse a subtree to a star phylogeny
Attaches a new tip to a tree
Fit diversity-dependent phenotypic evolution model
Interactive tree visualizer
Fits Mk model
Locate a fossil lineage in a tree using continuous characters
Add labels to subtrees of a plotted phylogeny
Collapse or resolve polytomies in a tree with a character painted on the edges
Summarizes a stochastic mapped tree or set of trees
Drop tip or tips from an object of class "contMap" or "densityMap"
Drop all the leaves (tips) from a tree
Converts a tree without singletons to a tree with singleton nodes
Locate a cryptic, recently extinct, or missing taxon on a tree
Compute an average tree from a set of trees and related operations
Simulates and visualizes discrete-time Brownian evolution on a phylogeny
Likelihood test for rate variation in a continuous trait
Estimate diversity at each node of the tree
Plots a posterior sample of trees
Animation of branching random diffusion
Plot posterior density of stochastic mapping on a tree
Generates (or simulates) a 'changes through time' plot from a set of stochastic map character histories
Bayesian MCMC method for identifying exceptional phenotypic diversification in a phylogeny
Expands (or contracts) the tip-spacing of a given clade or clades
Function to test for correlated evolution of binary traits
(Reasonably) fast estimation of ML ancestral states
Exhaustive and branch & bound MP optimization
(Reasonably) fast quantitative trait simulation on phylogenies
Adds a geological (or other temporal) legend to a plotted tree
Counts the number of character changes on a object of class "simmap" or "multiSimmap"
Computes a posterior distribution for the number and types of changes on the tree
Conducts a statistical test of cospeciation between two trees
Drop tips or extract clade from tree with mapped discrete character
Likelihood test for variation in the evolutionary variance-covariance matrix
Forces a phylogenetic tree to be ultrametric
Returns a vector, matrix, or list of the mapped states on a tree or set of trees
Ladderize a tree with a mapped discrete character
Get position or node of a plotted tree interactively
Finding the minimum (median) split in the posterior sample
Rotates all nodes of the tree to minimize the difference in order with a vector
Likelihood test for a shift in the evolutionary correlation between traits
Get the MRCA (or height above the root of the MRCA) of a pair of tip taxa
Plot phenogram (traitgram)
Lambda transformation of matrix
Phylogenetic regression with intraspecific sampling error
Compute the relative frequencies of state changes along edges
Likelihood for joint \(\lambda\)
Creates a (1-\(\alpha\))-percent CI for a set of LTTs
Plot branch colors by a quantitative trait or value
Merge two or more mapped states into one state
Create "era" map on a phylogenetic tree
Export trees & data in XML format
Get marginal ancestral state reconstructions by re-rooting
Read SIMMAP style trees from file
Phylogenetic paired t-test
Midpoint root a phylogeny
Phylogenetic reduced major axis (RMA) regression
Robust Newick style tree reader
Phylogenetic principal components analysis
Gamma test of Pybus & Harvey (2000)
Rescale SIMMAP style tree
Get the MRCA of a set of taxa
Plots backbone tree with triangles as clades
Matches nodes between two trees
Get descendant node numbers
Get all subtrees larger than or equal to a specified size
Phylogenetic canonical correlation analysis
Simulate a DNA alignment on the tree under a model
Plots special types of phylogenetic trees
Function to add tip labels to a plotted tree with linking lines
Set color map for various phylogenetic objects of classes
Converts tree to backbone or vice versa
Add marked changes to a plotted tree with mapped discrete character
Computes Robinson-Foulds distance between a set of trees
Get the states at nodes or tips from a mapped tree
Returns a list of the extant or extinct lineages in a tree containing non-contemporaneous tips
Function to interactively label nodes of a plotted tree
Compute the heights above the root of each node
Multiple matrix regression (partial Mantel test)
Add labels to a plotted "cophylo" object
Creates lineage-through-time plot (including extinct lineages)
Compute design matrix for least squares analyses
Creates phylomorphospace plot
Multivariate Brownian simulation with multiple correlations and rates
Least squares branch lengths for a given tree
Creates an animation of a tree growing from left-to-right or upwards
Slices the tree at a particular point and returns all subtrees, or the tree rootward of the point
Get the sister node number, label, or set of nodes for a node or tip
Phylogeny inference using the least squares method
Simulate stochastic character maps on a phylogenetic tree or trees
Returns a list with phylogenetic VCV matrix for each mapped state
Plot tree with tips linked to geographic coordinates
Computes modified Grafen edge lengths
Phylogenetic imputation for multivariate continuous character data
Creates tree-dimensional phylomorphospace plot
Paste two trees together
Proportional overlap between two mapped character histories on a tree
Paint sub-trees with a discrete character
Order the columns of mapped.edge to match across trees
Phylogenetic size-correction via GLS regression
Simulate pure-birth or birth-death stochastic tree or trees
Rounds the branch lengths of a tree
Compute evolutionary VCV matrix for a tree & dataset
Generic post-hoc test
Compute phylogenetic signal with two methods
Analysis of the posterior sample from evol.rate.mcmc
Matrix representation parsimony supertree estimation
Plot a round phylogram
Brownian or OU simulation with multiple evolutionary regimes
Phylogenetic ANOVA and post-hoc tests
Split tree at a point
Creates a graphical illustration of Brownian motion evolution on a phylogeny
Plot a tree with a discrete character data matrix at the tips
Plots rooted phylogenetic tree
Plots a phylogeny in two columns
Print method for backbone phylogeny
Creates a phylogenetic heat map
Plot stochastic character mapped tree
Tree plotting with posterior probabilities of ancestral states from the threshold model
Plot a tree with bars at the tips
Method for investigating the rate of one trait as a function of the state of another
Plot a tree with error bars around divergence dates
Reorders a backbone phylogeny
Replicate a tree or set of trees
Re-root a tree along an edge
Split edge colors when descendant edges have different mapped states
Matrix comparison using the method of random skewers
Reorder edges of a simmap tree
Threshold model using Bayesian MCMC
Conduct simulation of state dependent rate variation
Deviance Information Criterion from the threshold model
Computes value for a threshold character from a liability and thresholds
Find the temporal position of one or more rate shifts
Simulate character history or a discrete character at the tips of the tree under some model
Write a stochastic character mapped tree to file
phytools: Phylogenetic Tools for comparative biology (and other things)
Compute all possible resolutions of a node or all nodes in a multifurcating tree
Likelihood test for rate variation among trees, clades, or traits
Write a tree to file with ancestral states and (optionally) CIs at nodes
Convert a character vector to a binary matrix
Rotates a node or set of nodes in a phylogenetic tree
Calculates cophenetic (i.e., phylogenetic VCV) matrix
Attempts to untangle crossing branches for plotting
Pick a random state according to a vector of probabilities
Sample from a set of distributions
Create star phylogeny
Computes Strahler number for trees and nodes
Write a tree to file in Nexus format
Add species to genus on a phylogeny or bind simulated species subtrees to a backbone genus tree
Add an arrow pointing to a tip or node on the tree
Add color bar to a plot
Conducts correlational D-test from stochastic mapping
Computes AIC weights
Add tip to all edges in a tree
Generate all bi- and multifurcating unrooted trees
Add tips at random to the tree
Add legend to stochastically mapped tree