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