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