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