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