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