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