A B C D E F G H I K L M N O P R S T V W X Y Z
ace | Ancestral Character Estimation |
add.scale.bar | Add a Scale Bar to a Phylogeny Plot |
all.equal.phylo | Global Comparison of two Phylogenies |
as.hclust.phylo | Conversion Among Tree Objects |
as.matching | Conversion Between Phylo and Matching Objects |
as.phylo | Conversion Among Tree Objects |
as.phylo.matching | Conversion Between Phylo and Matching Objects |
as.phylo.phylog | Conversion Among Tree Objects |
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 |
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 |
chronogram | Chronogram Computed by Nonparametric Rate Smoothing |
coalescent.intervals | Coalescent Intervals |
coef.corBrownian | Brownian Correlation Structure |
coef.corGrafen | Grafen's (1989) Correlation Structure |
coef.corMartins | Martins's (1997) Correlation Structure |
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 |
corBrownian | Brownian Correlation Structure |
corClasses | Phylogenetic Correlation Structures |
corGrafen | Grafen's (1989) Correlation Structure |
corMartins | Martins's (1997) Correlation Structure |
corMatrix.corBrownian | Brownian Correlation Structure |
corMatrix.corGrafen | Grafen's (1989) Correlation Structure |
corMatrix.corMartins | Martins's (1997) Correlation Structure |
corPhyl | Phylogenetic Correlation Structures |
Correlogram | Compute a correlogram |
correlogram.formula | Compute a correlogram |
correlogram.phylo | Compute a correlogram |
di2multi | Collapse and Resolve Multichotomies |
discrete.dist | Taxonomic Level from a Pairwise Distances Matrix |
dist.dna | Pairwise Distances from DNA Sequences |
dist.gene | Pairwise Distances from Genetic Data |
dist.phylo | Pairwise Distances from a Phylogenetic Tree |
dist.taxo | Pairwise Distances from a Taxonomic Level |
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 |
extract.popsize | Reversible Jump MCMC to Infer Demographic History |
find.skyline.epsilon | Skyline Plot Estimate of Effective Population Size |
gammaStat | Gamma-Statistic of Pybus and Harvey |
GC.content | Content in GC from DNA Sequences |
H | Heterozygosity at a Locus Using Gene Frequencies |
heterozygosity | Heterozygosity at a Locus Using Gene Frequencies |
hivtree | Phylogenetic Tree of 193 HIV-1 Sequences |
howmanytrees | Calculate Numbers of Phylogenetic Trees |
Initialize.corPhyl | Initialize a 'corPhyl' Structure Object |
is.binary.tree | Test for Binary Tree |
is.rooted | Roots Phylogenetic Trees |
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 |
lines.popsize | Reversible Jump MCMC to Infer Demographic History |
lines.skyline | Drawing Skyline Plot Graphs |
ltt.lines | Lineages Through Time Plot |
ltt.plot | Lineages Through Time Plot |
mantel.test | Mantel Test for Similarity of Two Matrices |
mcmc.popsize | Reversible Jump MCMC to Infer Demographic History |
mltt.plot | Lineages Through Time Plot |
Moran.I | Moran's I Autocorrelation Index |
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 |
node.leafnumber | Get the Number of Leaves for a Node |
node.sons | Get the list of Sons for a Node |
nodelabels | Labelling the Nodes of a Tree |
NPRS.criterion | Objective Function Employed in Nonparametric Rate Smoothing |
nuc.div | Nucleotide Diversity |
opsin | Gene Tree of 32 opsin Sequences |
panel.superpose.correlogram | Lattice panel used in 'plot.correlogramList'. |
phymltest | Fits a Bunch of Models with PHYML |
pic | Phylogenetically Independent Contrasts |
plot.correlogram | Plot a Correlogram |
plot.correlogramList | Plot several Correlograms |
plot.mst | Minimum Spanning Tree |
plot.phylo | Plot Phylogenies |
plot.phymltest | Fits a Bunch of Models with PHYML |
plot.popsize | Reversible Jump MCMC to Infer Demographic History |
plot.skyline | Drawing Skyline Plot Graphs |
plot.varcomp | Plot Variance Components |
print.birthdeath | Estimation of Speciation and Extinction Rates With Birth-Death Models |
print.compar.gee | Comparative Analysis with GEEs |
print.phymltest | Fits a Bunch of Models with PHYML |
prop.clades | Tree Bipartition and Bootstrapping Phylogenies |
prop.part | Tree Bipartition and Bootstrapping Phylogenies |
ratogram | Ratogram Computed by Nonparametric Rate Smoothing |
rcoal | Generates Random Trees |
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 |
root | Roots Phylogenetic Trees |
rotate | Rotate an Internal Branch of a Tree |
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 |
summary.phylo | Print Summary of a Phylogeny |
summary.phymltest | Fits a Bunch of Models with PHYML |
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 |
varcomp | Compute Variance Component Estimates |
vcv.phylo | Phylogenetic Variance-covariance or Correlation 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.tree | Write Tree File in Parenthetic Format |
xenarthra | Molecular Phylogeny of Living Xenarthrans |
yule | Fits Yule Model to a Phylogenetic Tree |
yule.cov | Fits the Yule Model With Covariates |
zoom | Zoom on a Portion of a Phylogeny |