AAbin                   Amino Acid Sequences
CADM.global             Congruence among distance matrices
DNAbin                  Manipulate DNA Sequences in Bit-Level Format
DNAbin2indel            Recode Blocks of Indels
FastME                  Tree Estimation Based on the Minimum Evolution
                        Algorithm
Initialize.corPhyl      Initialize a 'corPhyl' Structure Object
LTT                     Theoretical Lineage-Through Time Plots
MPR                     Most Parsimonious Reconstruction
Moran.I                 Moran's I Autocorrelation Index
SDM                     Construction of Consensus Distance Matrix With
                        SDM
ace                     Ancestral Character Estimation
add.scale.bar           Add a Scale Bar to a Phylogeny Plot
additive                Incomplete Distance Matrix Filling
alex                    Alignment Explorer With Multiple Devices
all.equal.DNAbin        Compare DNA Sets
all.equal.phylo         Global Comparison of two Phylogenies
alview                  Print DNA or AA Sequence Alignement
ape-package             Analyses of Phylogenetics and Evolution
apetools                Tools to Explore Files
as.alignment            Conversion Among DNA Sequence Internal Formats
as.bitsplits            Split Frequencies and Conversion Among Split
                        Classes
as.matching             Conversion Between Phylo and Matching Objects
as.phylo                Conversion Among Tree and Network 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
bd.time                 Time-Dependent Birth-Death Models
binaryPGLMM             Phylogenetic Generalized Linear Mixed Model for
                        Binary Data
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
c.phylo                 Building Lists of Trees
carnivora               Carnivora body sizes and life history traits
checkAlignment          Check DNA Alignments
checkLabel              Checking Labels
checkValidPhylo         Check the Structure of a "phylo" Object
cherry                  Number of Cherries and Null Models of Trees
chiroptera              Bat Phylogeny
chronoMPL               Molecular Dating With Mean Path Lengths
chronopl                Molecular Dating With Penalized Likelihood
chronos                 Molecular Dating by Penalised Likelihood and
                        Maximum Likelihood
clustal                 Multiple Sequence Alignment with External
                        Applications
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
comparePhylo            Compare Two "phylo" Objects
compute.brlen           Branch Lengths Computation
compute.brtime          Compute and Set Branching Times
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
corphylo                Correlations among Multiple Traits with
                        Phylogenetic Signal
correlogram.formula     Phylogenetic Correlogram
data.nex                NEXUS Data Example
dbd                     Probability Density Under Birth-Death Models
def                     Definition of Vectors for Plotting or
                        Annotating
degree                  Vertex Degrees in Trees and Networks
del.gaps                Delete Alignment Gaps in DNA or AA Sequences
delta.plot              Delta Plots
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
diversity.contrast.test
                        Diversity Contrast Test
dnds                    dN/dS Ratio
drop.tip                Remove Tips in a Phylogenetic Tree
edges                   Draw Additional Edges on a Plotted Tree
evonet                  Evolutionary Networks
ewLasso                 Incomplete distances and edge weights of
                        unrooted topology
gammaStat               Gamma-Statistic of Pybus and Harvey
getAnnotationsGenBank   Read Annotations from GenBank
hivtree                 Phylogenetic Tree of 193 HIV-1 Sequences
howmanytrees            Calculate Numbers of Phylogenetic Trees
identify.phylo          Graphical Identification of Nodes and Tips
image.DNAbin            Plot of DNA Sequence Alignement
is.binary               Test for Binary Tree
is.compatible           Check Compatibility of Splits
is.monophyletic         Is Group Monophyletic
is.ultrametric          Test if a Tree is Ultrametric
kronoviz                Plot Multiple Chronograms on the Same Scale
label2table             Label Management
ladderize               Ladderize a Tree
latag2n                 Leading and Trailing Alignment Gaps to N
lmorigin                Multiple regression through the origin
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
mcconwaysims.test       McConway-Sims Test of Homogeneous
                        Diversification
mcmc.popsize            Reversible Jump MCMC to Infer Demographic
                        History
mixedFontLabel          Mixed Font Labels for Plotting
mrca                    Find Most Recent Common Ancestors Between Pairs
mst                     Minimum Spanning Tree
multi2di                Collapse and Resolve Multichotomies
multiphylo              Manipulating Lists of Trees
mvr                     Minimum Variance Reduction
nj                      Neighbor-Joining Tree Estimation
njs                     Tree Reconstruction from Incomplete Distances
                        With NJ* or bio-NJ*
node.dating             node.dating
node.depth              Depth and Heights of Nodes and Tips
nodelabels              Labelling the Nodes, Tips, and Edges of a Tree
nodepath                Find Paths of Nodes
parafit                 Test of host-parasite coevolution
pcoa                    Principal Coordinate Analysis
phydataplot             Tree Annotation
phymltest               Fits a Bunch of Models with PhyML
pic                     Phylogenetically Independent Contrasts
pic.ortho               Phylogenetically Independent Orthonormal
                        Contrasts
plot.correlogram        Plot a Correlogram
plot.phylo              Plot Phylogenies
plot.phylo.extra        Extra Fuctions to Plot and Annotate Phylogenies
plot.varcomp            Plot Variance Components
plotTreeTime            Plot Tree With Time Axis
print.phylo             Compact Display of a Phylogeny
rDNAbin                 Random DNA Sequences
rTraitCont              Continuous Character Simulation
rTraitDisc              Discrete Character Simulation
rTraitMult              Multivariate Character Simulation
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.gff                Read GFF Files
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
reconstruct             Continuous Ancestral Character Estimation
reorder.phylo           Internal Reordering of Trees
richness.yule.test      Test of Diversification-Shift With the Yule
                        Process
rlineage                Tree Simulation Under the Time-Dependent
                        Birth-Death Models
root                    Roots Phylogenetic Trees
rotate                  Swapping Sister Clades
rtree                   Generate Random Trees
rtt                     Root a Tree by Root-to-Tip Regression
seg.sites               Find Segregating Sites in DNA Sequences
skyline                 Skyline Plot Estimate of Effective Population
                        Size
skylineplot             Drawing Skyline Plot Graphs
slowinskiguyer.test     Slowinski-Guyer Test of Homogeneous
                        Diversification
solveAmbiguousBases     Solve Ambiguous Bases in DNA Sequences
speciesTree             Species Tree Estimation
stree                   Generates Systematic Regular Trees
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
trans                   Translation from DNA to Amino Acid Sequences
treePop                 Tree Popping
trex                    Tree Explorer With Multiple Devices
triangMtd               Tree Reconstruction Based on the Triangles
                        Method
unique.multiPhylo       Revomes Duplicate Trees
updateLabel             Update Labels
varCompPhylip           Variance Components with Orthonormal Contrasts
varcomp                 Compute Variance Component Estimates
vcv                     Phylogenetic Variance-covariance or Correlation
                        Matrix
vcv2phylo               Variance-Covariance Matrix to Tree
weight.taxo             Define Similarity Matrix
where                   Find Patterns in DNA Sequences
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.phyloXML          Write Tree File in phyloXML Format
write.tree              Write Tree File in Parenthetic Format
yule                    Fits the 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
