Analyses of Phylogenetics and Evolution


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Documentation for package `ape' version 1.7

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

-- A --

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

-- 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
boot.phylo Tree Bipartition and Bootstrapping Phylogenies
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
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

-- D --

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

-- 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
howmanytrees Calculate Numbers of Phylogenetic Trees

-- I --

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

-- 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
mrca Find Most Recent Common Ancestors Between Pairs
mst Minimum Spanning Tree
multi2di Collapse and Resolve Multichotomies

-- N --

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

-- O --

opsin Gene Tree of 32 opsin Sequences

-- P --

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

-- R --

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

-- 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
summary.phymltest Fits a Bunch of Models with PHYML

-- 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 --

varcomp Compute Variance Component Estimates
vcv.phylo Phylogenetic Variance-covariance or Correlation Matrix

-- W --

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

-- X --

xenarthra Molecular Phylogeny of Living Xenarthrans

-- Y --

yule Fits Yule Model to a Phylogenetic Tree
yule.cov Fits the Yule Model With Covariates

-- Z --

zoom Zoom on a Portion of a Phylogeny