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