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