Branching Times of a Phylogenetic Tree
Pairwise Distances from Genetic Data
Topological Distances Between Two Trees
Calculate Numbers of Phylogenetic Trees
Collapse Single Nodes
Carnivora body sizes and life history traits
Plot Ancestral Character Values on a Tree
Branch Lengths Computation
Neighbor-Joining Tree Estimation
Axis on Side of Phylogeny
Balance of a Dichotomous Phylogenetic Tree
Global Comparison of two Phylogenies
Cheverud's Comparative Method
Find Segregating Sites in DNA Sequences
Compute a correlogram
Collapsed Coalescent Intervals
Tests of Constant Diversification Rates
Phylogenetically Independent Contrasts
Compact Display of a Phylogeny
Phylogeny of the Orders of Birds From Sibley and Ahlquist
Objective Function Employed in Nonparametric Rate Smoothing
Analysis of Diversification with Survival Models
Concensus Trees
Lineages Through Time Plot
Phylogenetic Tree of 193 HIV-1 Sequences
Molecular Phylogeny of Living Xenarthrans
Rotate an Internal Branch of a Tree
Moran's I Autocorrelation Index
Ancestral Character Estimation
Plot a Correlogram
Read Character Data In NEXUS Format
Gene Tree of 36 Landplant rbcL Sequences
Conversion Among Tree Objects
Initialize a 'corPhyl' Structure Object
Coalescent Intervals
Binds Trees
Read DNA Sequences in a File
Internal Ape Functions
Generates Random Trees
Extended Version of the Birth-Death Models to Estimate Speciation
and Extinction Rates
Read Tree File in Nexus Format
Nucleotide Diversity
Martins's (1997) Correlation Structure
Compute Variance Component Estimates
Internal Reordering of Trees
Ornstein--Uhlenbeck Model for Continuous Characters
Read DNA Sequences from GenBank via Internet
Plot Variance Components
Bat Phylogeny
Heterozygosity at a Locus Using Gene Frequencies
Brownian Correlation Structure
Klastorin's (1982) method for classifying genes as suggested by Misawa
and Tajima (2000)
Depth of Nodes and Tips
Zoom on a Portion of a Phylogeny
Comparative Analysis with GEEs
Pairwise Distances from a Phylogenetic Tree
Skyline Plot Estimate of Effective Population Size
Phylogenetic Correlation Structures
Fits Yule Model to a Phylogenetic Tree
Write DNA Sequences in a File
Find Most Recent Common Ancestors Between Pairs
Identifies Edges of a Tree
Drawing Skyline Plot Graphs
Pairwise Distances from DNA Sequences
NEXUS Data Example
Conversion from Taxonomy Variables to Phylogenetic Trees
Remove Tips in a Phylogenetic Tree
Read Tree File in Parenthetic Format
Cytochrome b Gene Sequences of Woodmice
Plot Phylogenies
Write Tree File in Nexus Format
Tree Bipartition and Bootstrapping Phylogenies
Print Summary of a Phylogeny
Test if a Tree is Ultrametric
Minimum Spanning Tree
Reversible Jump MCMC to Infer Demographic History
Mantel Test for Similarity of Two Matrices
Population Parameter THETA using Segregating Sites
in DNA Sequences
Gamma-Statistic of Pybus and Harvey
Test for Binary Tree
panel.superpose.correlogram
Lattice panel used in 'plot.correlogramList'.
Collapse and Resolve Multichotomies
Ancestral Character Simulation
Pairwise Distances from a Taxonomic Level
Roots Phylogenetic Trees
Ratogram Computed by Nonparametric Rate Smoothing
Population Parameter THETA using Homozygosity
Fits the Yule Model With Covariates
Write Tree File in Parenthetic Format
Labelling the Nodes and the Tips of a Tree
Content in GC from DNA Sequences
Defines Models of DNA Evolution
Estimating Phylogenies by Maximum Likelihood
Population Parameter THETA using Expected Number of Alleles
Grafen's (1989) Correlation Structure
Base frequencies from DNA Sequences
Chronogram Computed by Nonparametric Rate Smoothing
Lynch's Comparative Method
Plot several Correlograms
Shimodaira-Hasegawa Test
Add a Scale Bar to a Phylogeny Plot
Molecular Dating With Penalized Likelihood
Fits a Bunch of Models with PHYML
Number of Cherries and Null Models of Trees
Phylogeny of the Families of Birds From Sibley and Ahlquist
Read Tree File in CAIC Format
Conversion Between Phylo and Matching Objects
Estimation of Speciation and Extinction Rates With Birth-Death Models
Taxonomic Level from a Pairwise Distances Matrix
Gene Tree of 32 opsin Sequences
Write Character Data In NEXUS Format
Phylogenetic Variance-covariance or Correlation Matrix
Ladderize a Tree