Phylogenetic Tools for Comparative Biology (and Other Things)
Computes a posterior distribution for the number and types of changes ...
Plot posterior density of stochastic mapping on a tree
Function to interactively label nodes of a plotted tree
Ladderize a tree with a mapped discrete character
transformation of matrix
Likelihood for joint
Function to add tip labels to a plotted tree with linking lines
Merge two or more mapped states into one state
Attempts to untangle crossing branches for plotting
Calculates cophenetic (i.e., phylogenetic VCV) matrix
Applies the branch lengths of a reference tree to a target
Conversion to object of class "multiPhylo"
Convert a fitted Mk model to a Q-matrix
Average the posterior rates
Compute the parsimony score
Drop tip or tips from an object of class "contMap" or "densityMap"
Drop or keep tip or tips from an object of class "multiSimmap"
Add an arrow pointing to a tip or node on the tree
Add color bar to a plot
Add tip to all edges in a tree
Add tips at random to the tree
Add legend to stochastically mapped tree
Add species to genus on a phylogeny or bind simulated species subtrees...
Computes Akaike weights
Generate all bi- and multifurcating unrooted trees
Bayesian ancestral character estimation
Ancestral character estimation using likelihood
Ancestral character estimation with a trend
Compute marginal or joint ancestral state estimates
Ancestral character estimation under the threshold model using Bayesia...
Compute an average tree from a set of trees and related operations
Convert object of class "birthdeath" to raw birth & death rates
Attaches a new tip to a tree
Binds two trees of class "simmap"
Simulates and visualizes discrete-time Brownian evolution on a phyloge...
Fits bounded and wrapped Brownian motion models
Compares two chronograms with precisely matching nodes in a visual man...
Animation of branching random diffusion
Likelihood test for rate variation in a continuous trait
REML version of brownie.lite
Add labels to subtrees of a plotted phylogeny
Collapse a subtree to a star phylogeny
Interactive tree visualizer
Compute consensus edges for a tree under some criterion
Map continuous trait evolution on the tree
Creates a co-phylogenetic plot
Conducts a statistical test of cospeciation between two trees
Counts the number of character changes on a object of class "simmap"...
Generates (or simulates) a 'changes through time' plot from a set of s...
Plots a posterior sample of trees
Summarizes a stochastic mapped tree or set of trees
Collapse or resolve polytomies in a tree with a character painted on t...
Creates a phylogenetic dot plot
Drop a clade from a tree
Drop all the leaves (tips) from a tree
Drop tips or extract clade from tree with mapped discrete character
Conducts correlational D-test from stochastic mapping
Map continuous trait evolution on the tree
Compute the relative frequencies of state changes along edges
Estimate diversity at each node of the tree
Bayesian MCMC method for identifying exceptional phenotypic diversific...
Likelihood test for variation in the evolutionary variance-covariance ...
Likelihood test for a shift in the evolutionary correlation between tr...
Exhaustive and branch & bound MP optimization
Expands (or contracts) the tip-spacing of a given clade or clades
Export trees & data in XML format
Plots special types of phylogenetic trees
(Reasonably) fast estimation of ML ancestral states
(Reasonably) fast quantitative trait simulation on phylogenies
Get the MRCA (or height above the root of the MRCA) of a pair of tip t...
Get the MRCA of a set of taxa
Fits birth-death (speciation/extinction) model to reconstructed phylog...
Evolutionary model fitting with intraspecific variability using Bayesi...
Fit diversity-dependent phenotypic evolution model
Fits extended Mk model for discrete character evolution
Fits bounded and wrapped Brownian motion models
Function to test for correlated evolution of binary traits
Fits multi-state threshold model using the discrete approximation
Coerces a phylogenetic tree to be ultrametric
Internally used function
Gamma test of Pybus & Harvey (2000)
Simulate a DNA alignment on the tree under a model
Get the states at nodes or tips from a mapped tree
Adds a geological (or other temporal) legend to a plotted tree
Get position or node of a plotted tree interactively
Get all subtrees larger than or equal to a specified size
Get descendant node numbers
Returns a list of the extant or extinct lineages in a tree containing ...
Get the sister node number, label, or set of nodes for a node or tip
Simulate stochastic character maps on a phylogenetic tree or trees
Locate a fossil lineage in a tree using continuous characters
Locate a cryptic, recently extinct, or missing taxon on a tree
Least squares branch lengths for a given tree
Creates lineage-through-time plot (including extinct lineages)
Creates a (1-)% CI for a set of LTTs
Create "era" map on a phylogenetic tree
Proportional overlap between two mapped character histories on a tree
Converts a tree without singletons to a tree with singleton nodes
Returns a vector, matrix, or list of the mapped states on a tree or se...
Add marked changes to a plotted tree with mapped discrete character
Matches nodes between two trees
Midpoint root a phylogeny
Rotates all nodes of the tree to minimize the difference in order with...
Finding the minimum (median) split in the posterior sample
Computes modified Grafen edge lengths
Reorder edges of a "simmap" tree
Matrix representation parsimony supertree estimation
Multiple matrix regression (partial Mantel test)
Returns a list with phylogenetic VCV matrix for each mapped state
Function to fit a multi-rate Brownian evolution model
Computes Robinson-Foulds distance between a set of trees
Phylogenetic paired t-test
Compute the heights above the root of each node
Add labels to a plotted "cophylo" object
Phylogeny inference using the least squares method
Order the columns of mapped.edge to match across trees
Phylogenetic principal components analysis
Paint sub-trees with a discrete character
Paste two trees together
Simulate pure-birth or birth-death stochastic tree or trees
Phylogenetic regression with intraspecific sampling error
Plot traitgram (phenogram)
Phylogenetic canonical correlation analysis
Generic post-hoc test
Print method for backbone phylogeny
Phylogenetic size-correction via GLS regression
Phylogenetic reduced major axis (RMA) regression
Compute evolutionary VCV matrix for a tree & dataset
Phylogenetic ANOVA and post-hoc tests
Replicate a tree or set of trees
Creates a phylogenetic heat map
Phylogenetic imputation for multivariate continuous character data
Plot tree with tips linked to geographic coordinates
Converts tree to backbone or vice versa
Compute design matrix for least squares analyses
Creates phylomorphospace plot
Creates three-dimensional phylomorphospace plot
Compute phylogenetic signal with two methods
Compute the parsimony score
phytools: Phylogenetic Tools for comparative biology (and other things...
Plots backbone tree with triangles as clades
Plot branch colors by a quantitative trait or value
Plot stochastic character mapped tree
Tree plotting with posterior probabilities of ancestral states from th...
Plot a tree with a discrete (or continuous) character data matrix at t...
Plot a tree with error bars around divergence dates
Plot a tree with one or more matched lollipop plots
Plots rooted phylogenetic tree
Plot a tree with bars at the tips
Analysis of the posterior sample from evol.rate.mcmc
Method for investigating the rate of one trait as a function of the st...
Likelihood test for rate variation among trees, clades, or traits
Find the temporal position of one or more rate shifts
Newick or Nexus style tree reader
Read SIMMAP style trees from file
Reorders a backbone phylogeny
Re-root a tree along an edge
Get marginal ancestral state reconstructions by re-rooting
Rescale phylogenetic objects of different types
Rescale object of class "simmap"
Compute all possible resolutions of a node or all nodes in a multifurc...
Rotates a node or set of nodes in a phylogenetic tree
Rounds the branch lengths of a tree
Plot a round, sigmoidal, or spline phylogram or cladogram
Pick a random state according to a vector of probabilities
Sample from a set of distributions
Set color map for various phylogenetic objects of classes
Multivariate Brownian simulation with multiple correlations and rates
Simulate character history or a discrete character at the tips of the ...
Conduct simulation of state dependent rate variation
Brownian or OU simulation with multiple evolutionary regimes
Creates a graphical illustration of Brownian motion evolution on a phy...
Matrix comparison using the method of random skewers
Split edge colors when descendant edges have different mapped states
Plots a phylogeny in two columns
Split tree at a point
Create star phylogeny
Computes Strahler number for trees and nodes
Threshold model using Bayesian MCMC
Deviance Information Criterion from the threshold model
Computes value for a threshold character from a liability and threshol...
Convert a character vector to a binary matrix
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...
Write a stochastic character mapped tree to file
Write a tree to file with ancestral states and (optionally) CIs at nod...
Write a tree to file in Nexus format
A wide range of methods for phylogenetic analysis - concentrated in phylogenetic comparative biology, but also including numerous techniques for visualizing, analyzing, manipulating, reading or writing, and even inferring phylogenetic trees. Included among the functions in phylogenetic comparative biology are various for ancestral state reconstruction, model-fitting, and simulation of phylogenies and trait data. A broad range of plotting methods for phylogenies and comparative data include (but are not restricted to) methods for mapping trait evolution on trees, for projecting trees into phenotype space or a onto a geographic map, and for visualizing correlated speciation between trees. Lastly, numerous functions are designed for reading, writing, analyzing, inferring, simulating, and manipulating phylogenetic trees and comparative data. For instance, there are functions for computing consensus phylogenies from a set, for simulating phylogenetic trees and data under a range of models, for randomly or non-randomly attaching species or clades to a tree, as well as for a wide range of other manipulations and analyses that phylogenetic biologists might find useful in their research.