GC.content              Content in GC from DNA Sequences
add.scale.bar           Add a Scale Bar to a Phylogeny Plot
all.equal.phylo         Global Comparison of two Phylogenies
ape-internal            Internal Ape Functions
balance                 Balance of a Dichotomous Phylogenetic Tree
base.freq               Base frequencies from DNA Sequences
bird.families           Phylogeny of the Families of Birds From Sibley
                        and Ahlquist
birthdeath              Estimation of Speciation and Extinction Rates
                        With Birth-Death Models
branching.times         Branching Times of a Phylogenetic Tree
cherry                  Number of Cherries and Null Models of Trees
coalescent.intervals    Coalescent Intervals
collapsed.intervals     Collapsed Coalescent Intervals
compar.gee              Comparative Analysis with GEEs
compar.lynch            Lynch's Comparative Method
dist.dna                Pairwise Distances from DNA Sequences
dist.gene               Pairwise Distances from Genetic Data
dist.phylo              Pairwise Distances from a Phylogenetic Tree
diversi.gof             Tests of Constant Diversification Rates
diversi.time            Analysis of Diversification with Survival
                        Models
gamma.stat              Gamma-Statistic of Pybus and Harvey
heterozygosity          Heterozygosity at a Locus Using Gene
                        Frequencies
hivtree                 Phylogenetic Tree of 193 HIV-1 Sequences
is.binary.tree          Test for Binary Tree
ltt.plot                Lineages Through Time Plot
mantel.test             Mantel Test for Similarity of Two Matrices
mst                     Minimum Spanning Tree
pic                     Phylogenetically Independent Contrasts
plot.phylo              Plot Phylogenies
read.GenBank            Read DNA Sequences from GenBank via Internet
read.tree               Read Tree File in Parenthetic Format
skyline                 Skyline Plot Estimate of Effective Population
                        Size
skylineplot             Drawing Skyline Plot Graphs
theta.h                 Population Parameter THETA using Homozygosity
theta.k                 Population Parameter THETA using Expected
                        Number of Alleles
theta.s                 Population Parameter THETA using Segregating
                        Sites in DNA Sequences
vcv.phylo               Phylogenetic Variance-covariance or Correlation
                        Matrix
write.tree              Write Tree File in Parenthetic Format