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