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