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