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