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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
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
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
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
del.gaps Delete Alignment Gaps in DNA 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
drop.tip Remove Tips in a Phylogenetic Tree
edges Draw Additional Edges on a Plotted Tree
estimate.mu node.dating
evonet Evolutionary Networks
ewLasso Incomplete distances and edge weights of
unrooted topology
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
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
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.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
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 Generates 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
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
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.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
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