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