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