Tests of Constant Diversification Rates
Five Trees
Plot Variance Components
Test of host-parasite coevolution
Manipulate DNA Sequences in Bit-Level Format
Pairwise Distances from a Phylogenetic Tree
Phylogenetic Correlogram
Gamma-Statistic of Pybus and Harvey
Cheverud's Comparative Method
Read Character Data In NEXUS Format
Number of Cherries and Null Models of Trees
Phylogeny of the Orders of Birds From Sibley and Ahlquist
Concensus Trees
Manipulating Lists of Trees
Phylogenetically Independent Orthonormal Contrasts
Principal Coordinate Analysis
Is Group Monophyletic
Draw Additional Edges on a Plotted Tree
Most Parsimonious Reconstruction
Phylogeny of the Families of Birds From Sibley and Ahlquist
Conversion Between Phylo and Matching Objects
Brownian Correlation Structure
Grafen's (1989) Correlation Structure
Collapsed Coalescent Intervals
Binds Trees
NEXUS Data Example
Building Lists of Trees
Analysis of Diversification with Survival Models
Branch Lengths Computation
Plot a Correlogram
Collapse and Resolve Multichotomies
Variance Components with Orthonormal Contrasts
Pairwise Distances from DNA Sequences
Zoom on a Portion of a Phylogeny by Successive Clicks
Write DNA Sequences in a File
Write Tree File in Nexus Format
Mixed Font Labels for Plotting
Base frequencies from DNA Sequences
Pairwise Distances from Genetic Data
Tree Estimation Based on an Improved Version of the NJ Algorithm
All subtrees of a Phylogenetic Tree
Topological Distances Between Two Trees
Gene Tree of 32 opsin Sequences
Conversion Among DNA Sequence Internal Formats
Moran's I Autocorrelation Index
Phylogenetic Correlation Structures
Molecular Dating With Mean Path Lengths
Collapse Single Nodes
Carnivora body sizes and life history traits
Content in GC from DNA Sequences
Ornstein--Uhlenbeck Model for Continuous Characters
Tree Estimation Based on the Minimum Evolution Algorithm
Mantel Test for Similarity of Two Matrices
Cytochrome b Gene Sequences of Woodmice
Conversion Among Tree Objects
Graphical Identification of Nodes and Tips
Martins's (1997) Correlation Structure
Congruence among distance matrices
Read DNA Sequences in a File
Compute Variance Component Estimates
Five Independent Trees
Three Matrices
Defunct Ape Functions
Balance of a Dichotomous Phylogenetic Tree
Test for Binary Tree
Lynch's Comparative Method
Estimation of Speciation and Extinction Rates With Birth-Death Models
Ladderize a Tree
Read Tree File in CAIC Format
Global Comparison of two Phylogenies
Ancestral Character Estimation
Tree Simulation Under the Time-Dependent Birth--Death Models
Identifies Edges of a Tree
Makes Node Labels
Internal Reordering of Trees
Generates Systematic Regular Trees
Remove Tips in a Phylogenetic Tree
Add a Scale Bar to a Phylogeny Plot
Neighbor-Joining Tree Estimation
Species Tree Estimation
Swapping sister clades
Discrete Character Simulation
Comparative Analysis with GEEs
Tree Bipartition and Bootstrapping Phylogenies
Multiple regression through the origin
Continuous Character Simulation
Write Tree File in Parenthetic Format
Read Tree File in Parenthetic Format
Fits Yule Model to a Phylogenetic Tree
Axis on Side of Phylogeny
Internal Ape Functions
Reversible Jump MCMC to Infer Demographic History
Bat Phylogeny
Molecular Dating With Penalized Likelihood
Coalescent Intervals
Labelling the Nodes, Tips, and Edges of a Tree
Delta Plots
Plots two phylogenetic trees face to face with links between the tips.
Define Similarity Matrix
Roots Phylogenetic Trees
Depth of Nodes and Tips
Find Segregating Sites in DNA Sequences
Minimum Spanning Tree
Fits a Bunch of Models with PhyML
Drawing Skyline Plot Graphs
Fits the Time-Dependent Yule Model
Extended Version of the Birth-Death Models to Estimate Speciation
and Extinction Rates
Fits the Yule Model With Covariates
Compact Display of a Phylogeny
Delete Alignment Gaps in DNA Sequences
Label Management
Lineages Through Time Plot
Print Summary of a Phylogeny
Phylogenetically Independent Contrasts
Matrix Exponential
Gene Tree of 36 Landplant rbcL Sequences
Read Tree File in Nexus Format
Pagel's ``lambda'' Correlation Structure
Revomes Duplicate Trees
Find Most Recent Common Ancestors Between Pairs
Skyline Plot Estimate of Effective Population Size
Plot Phylogenies
Phylogenetic Variance-covariance or Correlation Matrix
Branching Times of a Phylogenetic Tree
Write Character Data In NEXUS Format
Test if a Tree is Ultrametric
Generates Random Trees
Blomberg et al.'s Correlation Structure
Time-Dependent Birth-Death Models
Analyses of Phylogenetics and Evolution
Zoom on a Portion of a Phylogeny
Read DNA Sequences from GenBank via Internet
Initialize a `corPhyl' Structure Object
Conversion from Taxonomy Variables to Phylogenetic Trees
Phylogenetic Tree of 193 HIV-1 Sequences
Calculate Numbers of Phylogenetic Trees