Analyses of Phylogenetics and Evolution


[Package List] [Top]

A B C D E F G H I K L M N O P R S T V W X Y Z

-- A --

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

-- B --

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

-- C --

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

-- D --

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

-- E --

extract.popsize Reversible Jump MCMC to Infer Demographic History

-- F --

find.skyline.epsilon Skyline Plot Estimate of Effective Population Size

-- G --

gammaStat Gamma-Statistic of Pybus and Harvey
GC.content Content in GC from DNA Sequences

-- H --

H Heterozygosity at a Locus Using Gene Frequencies
heterozygosity Heterozygosity at a Locus Using Gene Frequencies
hivtree Phylogenetic Tree of 193 HIV-1 Sequences

-- I --

is.binary.tree Test for Binary Tree
is.ultrametric Test if a Tree is Ultrametric

-- K --

klastorin Klastorin's (1982) method for classifying genes as suggested by Misawa and Tajima (2000)

-- L --

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

-- M --

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

-- N --

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

-- O --

opsin Gene Tree of 32 opsin Sequences

-- P --

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

-- R --

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

-- S --

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

-- T --

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

-- V --

vcv.phylo Phylogenetic Variance-covariance or Correlation Matrix

-- W --

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

-- X --

xenarthra Molecular Phylogeny of Living Xenarthrans

-- Y --

yule Fits Yule Model to a Phylogenetic Tree

-- Z --

zoom Zoom on a Portion of a Phylogeny