Analyses of Phylogenetics and Evolution


[Package List] [Top]

Documentation for package ‘ape’ version 2.3

User Guides and Package Vignettes

Read overview or browse directory.

Help Pages

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

-- --

ape-package Analyses of Phylogenetics and Evolution

-- --

$.multiPhylo Compact Display of a Phylogeny

-- A --

ace Ancestral Character Estimation
add.scale.bar Add a Scale Bar to a Phylogeny Plot
AIC.ace Ancestral Character Estimation
AIC.phylo Estimating Phylogenies by Maximum Likelihood
all.equal.phylo Global Comparison of two Phylogenies
anova.ace Ancestral Character Estimation
ape Analyses of Phylogenetics and Evolution
as.alignment Conversion Among DNA Sequence Internal Formats
as.character.DNAbin Conversion Among DNA Sequence Internal Formats
as.DNAbin Conversion Among DNA Sequence Internal Formats
as.hclust.phylo Conversion Among Tree Objects
as.matching Conversion Between Phylo and Matching Objects
as.matrix.DNAbin Manipulate DNA Sequences in Bit-Level Format
as.phylo Conversion Among Tree Objects
as.phylo.formula Conversion from Taxonomy Variables to Phylogenetic Trees
as.phylo.hclust 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
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 --

CADM.global Congruence among distance matrices
CADM.post Congruence among distance matrices
carnivora Carnivora body sizes and life history traits
cbind.DNAbin Manipulate DNA Sequences in Bit-Level Format
cherry Number of Cherries and Null Models of Trees
chiroptera Bat Phylogeny
chronogram Chronogram Computed by Nonparametric Rate Smoothing
chronoMPL Molecular Dating With Mean Path Lengths
chronopl Molecular Dating With Penalized Likelihood
coalescent.intervals Coalescent Intervals
coef.corBlomberg Blomberg et al.'s Correlation Structure
coef.corBrownian Brownian Correlation Structure
coef.corGrafen Grafen's (1989) Correlation Structure
coef.corMartins Martins's (1997) Correlation Structure
coef.corPagel Pagel's “lambda” Correlation Structure
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
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
corMatrix.corBlomberg Blomberg et al.'s Correlation Structure
corMatrix.corBrownian Brownian Correlation Structure
corMatrix.corGrafen Grafen's (1989) Correlation Structure
corMatrix.corMartins Martins's (1997) Correlation Structure
corMatrix.corPagel Pagel's “lambda” Correlation Structure
corPagel Pagel's “lambda” Correlation Structure
corPhyl Phylogenetic Correlation Structures
correlogram.formula Phylogenetic Correlogram
cynipids NEXUS Data Example

-- D --

data.nex NEXUS Data Example
del.gaps Delete Alignment Gaps in DNA Sequences
deviance.ace Ancestral Character Estimation
deviance.phylo Estimating Phylogenies by Maximum Likelihood
di2multi Collapse and Resolve Multichotomies
dist.dna Pairwise Distances from DNA Sequences
dist.gene Pairwise Distances from Genetic Data
dist.nodes Pairwise Distances from a Phylogenetic Tree
dist.topo Topological Distances Between Two Trees
diversi.gof Tests of Constant Diversification Rates
diversi.time Analysis of Diversification with Survival Models
DNAbin Manipulate DNA Sequences in Bit-Level Format
DNAmodel Defines Models of DNA Evolution
drop.tip Remove Tips in a Phylogenetic Tree
drop1.compar.gee Comparative Analysis with GEEs

-- E --

edgelabels Labelling the Nodes, Tips, and Edges of a Tree
evolve.phylo Ancestral Character Simulation
extract.clade Remove Tips in a Phylogenetic Tree
extract.popsize Reversible Jump MCMC to Infer Demographic History

-- F --

fastme Tree Estimation Based on the Minimum Evolution Algorithm
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 --

identify.phylo Graphical Identification of Nodes and Tips
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 --

ladderize Ladderize a Tree
landplants Gene Tree of 36 Landplant rbcL Sequences
lines.popsize Reversible Jump MCMC to Infer Demographic History
lines.skyline Drawing Skyline Plot Graphs
logLik.ace Ancestral Character Estimation
logLik.phylo Estimating Phylogenies by Maximum Likelihood
ltt.lines Lineages Through Time Plot
ltt.plot Lineages Through Time Plot

-- M --

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
mcmc.popsize Reversible Jump MCMC to Infer Demographic History
mlphylo Estimating Phylogenies by Maximum Likelihood
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 --

Nedge Print Summary of a Phylogeny
new2old.phylo Conversion Among Tree Objects
nj Neighbor-Joining Tree Estimation
Nnode Print Summary of a Phylogeny
node.depth Depth of Nodes and Tips
nodelabels Labelling the Nodes, Tips, and Edges of a Tree
NPRS.criterion Objective Function Employed in Nonparametric Rate Smoothing
Ntip Print Summary of a Phylogeny
nuc.div Nucleotide Diversity

-- O --

old2new.phylo Conversion Among Tree Objects
opsin Gene Tree of 32 opsin Sequences

-- P --

phymltest Fits a Bunch of Models with PhyML
pic Phylogenetically Independent Contrasts
plot.ancestral Plot Ancestral Character Values on a Tree
plot.correlogram Plot a Correlogram
plot.correlogramList Plot a Correlogram
plot.mst Minimum Spanning Tree
plot.multiPhylo Plot Phylogenies
plot.phylo Plot Phylogenies
plot.phymltest Fits a Bunch of Models with PhyML
plot.popsize Reversible Jump MCMC to Infer Demographic History
plot.prop.part Tree Bipartition and Bootstrapping Phylogenies
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.DNAbin Manipulate DNA Sequences in Bit-Level Format
print.multiPhylo Compact Display of a Phylogeny
print.phylo Compact Display of a Phylogeny
print.phymltest Fits a Bunch of Models with PhyML
print.prop.part Tree Bipartition and Bootstrapping Phylogenies
prop.clades Tree Bipartition and Bootstrapping Phylogenies
prop.part Tree Bipartition and Bootstrapping Phylogenies

-- R --

ratogram Ratogram Computed by Nonparametric Rate Smoothing
rbind.DNAbin Manipulate DNA Sequences in Bit-Level Format
rcoal Generates Random Trees
read.caic Read Tree File in CAIC Format
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.nexus.data Read Character Data In NEXUS Format
read.tree Read Tree File in Parenthetic Format
reorder.phylo Internal Reordering of Trees
rmtree Generates Random Trees
root Roots Phylogenetic Trees
rotate Swapping sister clades
rtree Generates Random Trees

-- S --

seg.sites Find Segregating Sites in DNA Sequences
sh.test Shimodaira-Hasegawa Test
skyline Skyline Plot Estimate of Effective Population Size
skylineplot Drawing Skyline Plot Graphs
str.multiPhylo Compact Display of a Phylogeny
subtreeplot Zoom on a Portion of a Phylogeny by Successive Clicks
subtrees All subtrees of a Phylogenetic Tree
summary.DNAbin Manipulate DNA Sequences in Bit-Level Format
summary.phylo Print Summary of a Phylogeny
summary.phymltest Fits a Bunch of Models with PhyML
summary.prop.part Tree Bipartition and Bootstrapping Phylogenies

-- 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
tiplabels Labelling the Nodes, Tips, and Edges of a Tree

-- U --

unique.multiPhylo Revomes Duplicate Trees
unroot Roots Phylogenetic Trees

-- V --

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

-- W --

weight.taxo Define Similarity Matrix
weight.taxo2 Define Similarity 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.nexus.data Write Character Data In NEXUS Format
write.tree Write Tree File in Parenthetic Format

-- Y --

yule Fits Yule Model to a Phylogenetic Tree
yule.cov Fits the Yule Model With Covariates
yule.time Fits the Time-Dependent Yule Model

-- Z --

zoom Zoom on a Portion of a Phylogeny

-- misc --

[.DNAbin Manipulate DNA Sequences in Bit-Level Format
[.multiPhylo Compact Display of a Phylogeny
[[.multiPhylo Compact Display of a Phylogeny