A B C D E F G H I K L M N O P R S T V W X Y Z
add.scale.bar | Add a Scale Bar to a Phylogeny Plot |
all.equal.phylo | Global Comparison of two Phylogenies |
as.hclust.phylo | Conversion between "phylo" and "hclust" trees |
as.phylo | Conversion between "phylo" and "hclust" trees |
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 |
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 |
collapsed.intervals | Collapsed Coalescent Intervals |
compar.gee | Comparative Analysis with GEEs |
compar.lynch | Lynch's Comparative Method |
Correlogram | Compute a correlogram |
correlogram.formula | Compute a correlogram |
correlogram.phylo | Compute a correlogram |
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 |
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 |
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 |
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 |
mst | Minimum Spanning Tree |
node.depth | Depth of Nodes and Tips |
node.depth.edgelength | Distance from Root to Nodes and Tips |
NPRS.criterion | Objective Function Employed in Nonparametric Rate Smoothing |
opsin | Gene Tree of 32 opsin Sequences |
pic | Phylogenetically Independent Contrasts |
plot.correlogram | Plot a Correlogram |
plot.mst | Minimum Spanning Tree |
plot.phylo | Plot Phylogenies |
plot.popsize | Reversible Jump MCMC to Infer Demographic History |
plot.skyline | Drawing Skyline Plot Graphs |
print.compar.gee | Comparative Analysis with GEEs |
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 |
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 |
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 |
woodmouse | Cytochrome b 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 |
zoom | Zoom on a Portion of a Phylogeny |