CADM.global             Congruence among distance matrices
DNAbin                  Manipulate DNA Sequences in Bit-Level Format
GC.content              Content in GC from DNA Sequences
Initialize.corPhyl      Initialize a 'corPhyl' Structure Object
Moran.I                 Moran's I Autocorrelation Index
NPRS.criterion          Objective Function Employed in Nonparametric
                        Rate Smoothing
ace                     Ancestral Character Estimation
add.scale.bar           Add a Scale Bar to a Phylogeny Plot
all.equal.phylo         Global Comparison of two Phylogenies
ape-package             Analyses of Phylogenetics and Evolution
as.alignment            Conversion Among DNA Sequence Internal Formats
as.matching             Conversion Between Phylo and Matching Objects
as.phylo                Conversion Among Tree Objects
as.phylo.formula        Conversion from Taxonomy Variables to
                        Phylogenetic Trees
axisPhylo               Axis on Side of Phylogeny
balance                 Balance of a Dichotomous Phylogenetic Tree
base.freq               Base frequencies from DNA Sequences
bd.ext                  Extended Version of the Birth-Death Models to
                        Estimate Speciation and Extinction Rates
bind.tree               Binds Trees
bionj                   Tree Estimation Based on an Improved Version of
                        the NJ Algorithm
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
boot.phylo              Tree Bipartition and Bootstrapping Phylogenies
branching.times         Branching Times of a Phylogenetic Tree
carnivora               Carnivora body sizes and life history traits
cherry                  Number of Cherries and Null Models of Trees
chiroptera              Bat Phylogeny
chronoMPL               Molecular Dating With Mean Path Lengths
chronogram              Chronogram Computed by Nonparametric Rate
                        Smoothing
chronopl                Molecular Dating With Penalized Likelihood
coalescent.intervals    Coalescent Intervals
collapse.singles        Collapse Single Nodes
collapsed.intervals     Collapsed Coalescent Intervals
compar.cheverud         Cheverud's Comparative Method
compar.gee              Comparative Analysis with GEEs
compar.lynch            Lynch's Comparative Method
compar.ou               Ornstein-Uhlenbeck Model for Continuous
                        Characters
compute.brlen           Branch Lengths Computation
consensus               Concensus Trees
cophenetic.phylo        Pairwise Distances from a Phylogenetic Tree
cophyloplot             Plots two phylogenetic trees face to face with
                        links between the tips.
corBlomberg             Blomberg et al.'s Correlation Structure
corBrownian             Brownian Correlation Structure
corClasses              Phylogenetic Correlation Structures
corGrafen               Grafen's (1989) Correlation Structure
corMartins              Martins's (1997) Correlation Structure
corPagel                Pagel's "lambda" Correlation Structure
correlogram.formula     Phylogenetic Correlogram
data.nex                NEXUS Data Example
del.gaps                Delete Alignment Gaps in DNA Sequences
dist.dna                Pairwise Distances from DNA Sequences
dist.gene               Pairwise Distances from Genetic Data
dist.topo               Topological Distances Between Two Trees
diversi.gof             Tests of Constant Diversification Rates
diversi.time            Analysis of Diversification with Survival
                        Models
drop.tip                Remove Tips in a Phylogenetic Tree
evolve.phylo            Ancestral Character Simulation
fastme                  Tree Estimation Based on the Minimum Evolution
                        Algorithm
gammaStat               Gamma-Statistic of Pybus and Harvey
hivtree                 Phylogenetic Tree of 193 HIV-1 Sequences
howmanytrees            Calculate Numbers of Phylogenetic Trees
identify.phylo          Graphical Identification of Nodes and Tips
is.binary.tree          Test for Binary Tree
is.monophyletic         Is Group Monophyletic
is.ultrametric          Test if a Tree is Ultrametric
ladderize               Ladderize a Tree
landplants              Gene Tree of 36 Landplant rbcL Sequences
ltt.plot                Lineages Through Time Plot
makeLabel               Label Management
makeNodeLabel           Makes Node Labels
mantel.test             Mantel Test for Similarity of Two Matrices
mat3                    Three Matrices
mat5M3ID                Five Trees
mat5Mrand               Five Independent Trees
matexpo                 Matrix Exponential
mcmc.popsize            Reversible Jump MCMC to Infer Demographic
                        History
mrca                    Find Most Recent Common Ancestors Between Pairs
mst                     Minimum Spanning Tree
multi2di                Collapse and Resolve Multichotomies
nj                      Neighbor-Joining Tree Estimation
node.depth              Depth of Nodes and Tips
nodelabels              Labelling the Nodes, Tips, and Edges of a Tree
opsin                   Gene Tree of 32 opsin Sequences
phymltest               Fits a Bunch of Models with PhyML
pic                     Phylogenetically Independent Contrasts
plot.ancestral          Plot Ancestral Character Values on a Tree
plot.correlogram        Plot a Correlogram
plot.phylo              Plot Phylogenies
plot.varcomp            Plot Variance Components
print.phylo             Compact Display of a Phylogeny
ratogram                Ratogram Computed by Nonparametric Rate
                        Smoothing
read.GenBank            Read DNA Sequences from GenBank via Internet
read.caic               Read Tree File in CAIC Format
read.dna                Read DNA Sequences in a File
read.nexus              Read Tree File in Nexus Format
read.nexus.data         Read Character Data In NEXUS Format
read.tree               Read Tree File in Parenthetic Format
reorder.phylo           Internal Reordering of Trees
root                    Roots Phylogenetic Trees
rotate                  Swapping sister clades
rtree                   Generates Random Trees
seg.sites               Find Segregating Sites in DNA Sequences
skyline                 Skyline Plot Estimate of Effective Population
                        Size
skylineplot             Drawing Skyline Plot Graphs
subtreeplot             Zoom on a Portion of a Phylogeny by Successive
                        Clicks
subtrees                All subtrees of a Phylogenetic Tree
summary.phylo           Print Summary of a Phylogeny
unique.multiPhylo       Revomes Duplicate Trees
varcomp                 Compute Variance Component Estimates
vcv.phylo               Phylogenetic Variance-covariance or Correlation
                        Matrix
weight.taxo             Define Similarity Matrix
which.edge              Identifies Edges of a Tree
woodmouse               Cytochrome b Gene Sequences of Woodmice
write.dna               Write DNA Sequences in a File
write.nexus             Write Tree File in Nexus Format
write.nexus.data        Write Character Data In NEXUS Format
write.tree              Write Tree File in Parenthetic Format
yule                    Fits Yule Model to a Phylogenetic Tree
yule.cov                Fits the Yule Model With Covariates
yule.time               Fits the Time-Dependent Yule Model
zoom                    Zoom on a Portion of a Phylogeny
