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