add.scale.bar           Add a Scale Bar to a Phylogeny Plot
all.equal.phylo         Global Comparison of two Phylogenies
as.phylo                Conversion between "phylo" and "hclust" trees
balance                 Balance of a Dichotomous Phylogenetic Tree
base.freq               Base frequencies from DNA Sequences
bind.tree               Binds Trees
bird.families           Phylogeny of the Families of Birds From Sibley
                        and Ahlquist
bird.orders             Phylogeny of the Orders 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
chronogram              Chronogram Computed by Nonparametric Rate
                        Smoothing
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
drop.tip                Remove Tips in a Phylogenetic Tree
gamma.stat              Gamma-Statistic of Pybus and Harvey
GC.content              Content in GC from DNA Sequences
heterozygosity          Heterozygosity at a Locus Using Gene
                        Frequencies
hivtree                 Phylogenetic Tree of 193 HIV-1 Sequences
is.binary.tree          Test for Binary Tree
is.ultrametric          Test if a Tree is Ultrametric
klastorin               Klastorin's (1982) method for classifying
                        genes as suggested by Misawa and Tajima (2000)
landplants              Gene Tree of 36 Landplant rbcL Sequences
ltt.plot                Lineages Through Time Plot
mantel.test             Mantel Test for Similarity of Two Matrices
mst                     Minimum Spanning Tree
NPRS.criterion          Objective Function Employed in Nonparametric
                        Rate Smoothing
opsin                   Gene Tree of 32 opsin Sequences
pic                     Phylogenetically Independent Contrasts
plot.phylo              Plot Phylogenies
ratogram                Ratogram Computed by Nonparametric Rate
                        Smoothing
read.dna                Read DNA Sequences in a File
read.GenBank            Read DNA Sequences from GenBank via Internet
read.nexus              Read Tree File in Nexus Format
read.tree               Read Tree File in Parenthetic Format
skyline                 Skyline Plot Estimate of Effective Population
                        Size
skylineplot             Drawing Skyline Plot Graphs
summary.phylo           Print Summary of a Phylogeny
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.dna               Write DNA Sequences in a File
write.nexus             Write Tree File in Nexus Format
write.tree              Write Tree File in Parenthetic Format
xenarthra               Molecular Phylogeny of Living Xenarthrans