Analyses of Phylogenetics and Evolution


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Documentation for package ‘ape’ version 5.5

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

ape-package Analyses of Phylogenetics and Evolution

-- A --

AAbin Amino Acid Sequences
AAsubst Amino Acid Sequences
abbreviateGenus Label Management
ace Ancestral Character Estimation
add.scale.bar Add a Scale Bar to a Phylogeny Plot
additive Incomplete Distance Matrix Filling
AIC.ace Ancestral Character Estimation
alex Alignment Explorer With Multiple Devices
all.equal.DNAbin Compare DNA Sets
all.equal.phylo Global Comparison of two Phylogenies
alview Print DNA or AA Sequence Alignement
anova.ace Ancestral Character Estimation
ape Analyses of Phylogenetics and Evolution
apetools Tools to Explore Files
arecompatible Check Compatibility of Splits
as.AAbin Amino Acid Sequences
as.AAbin.AAMultipleAlignment Amino Acid Sequences
as.AAbin.AAString Amino Acid Sequences
as.AAbin.AAStringSet Amino Acid Sequences
as.AAbin.character Amino Acid Sequences
as.AAbin.list Amino Acid Sequences
as.alignment Conversion Among DNA Sequence Internal Formats
as.bitsplits Split Frequencies and Conversion Among Split Classes
as.bitsplits.prop.part Split Frequencies and Conversion Among Split Classes
as.character.AAbin Amino Acid Sequences
as.character.DNAbin Conversion Among DNA Sequence Internal Formats
as.DNAbin Conversion Among DNA Sequence Internal Formats
as.DNAbin.alignment Conversion Among DNA Sequence Internal Formats
as.DNAbin.character Conversion Among DNA Sequence Internal Formats
as.DNAbin.DNAMultipleAlignment Conversion Among DNA Sequence Internal Formats
as.DNAbin.DNAString Conversion Among DNA Sequence Internal Formats
as.DNAbin.DNAStringSet Conversion Among DNA Sequence Internal Formats
as.DNAbin.list Conversion Among DNA Sequence Internal Formats
as.DNAbin.PairwiseAlignmentsSingleSubject Conversion Among DNA Sequence Internal Formats
as.evonet Evolutionary Networks
as.evonet.phylo Evolutionary Networks
as.hclust.phylo Conversion Among Tree and Network Objects
as.igraph Conversion Among Tree and Network Objects
as.igraph.evonet Evolutionary Networks
as.igraph.phylo Conversion Among Tree and Network Objects
as.list.AAbin Amino Acid Sequences
as.list.DNAbin Manipulate DNA Sequences in Bit-Level Format
as.matching Conversion Between Phylo and Matching Objects
as.matching.phylo Conversion Between Phylo and Matching Objects
as.matrix.AAbin Amino Acid Sequences
as.matrix.DNAbin Manipulate DNA Sequences in Bit-Level Format
as.network.evonet Evolutionary Networks
as.network.phylo Conversion Among Tree and Network Objects
as.networx.evonet Evolutionary Networks
as.phyDat.AAbin Amino Acid Sequences
as.phylo Conversion Among Tree and Network Objects
as.phylo.evonet Evolutionary Networks
as.phylo.formula Conversion from Taxonomy Variables to Phylogenetic Trees
as.phylo.hclust Conversion Among Tree and Network Objects
as.phylo.matching Conversion Between Phylo and Matching Objects
as.phylo.phylog Conversion Among Tree and Network Objects
as.prop.part Split Frequencies and Conversion Among Split Classes
as.prop.part.bitsplits Split Frequencies and Conversion Among Split Classes
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
bd.time Time-Dependent Birth-Death Models
binaryPGLMM Phylogenetic Generalized Linear Mixed Model for Binary Data
binaryPGLMM.sim Phylogenetic Generalized Linear Mixed Model for Binary Data
bind.tree Binds Trees
bionj Tree Estimation Based on an Improved Version of the NJ Algorithm
bionjs Tree Reconstruction from Incomplete Distances With NJ* or bio-NJ*
biplot.pcoa Principal Coordinate Analysis
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
bitsplits Split Frequencies and Conversion Among Split Classes
boot.phylo Tree Bipartition and Bootstrapping Phylogenies
branching.times Branching Times of a Phylogenetic Tree
bydir Tools to Explore Files

-- C --

c.AAbin Amino Acid Sequences
c.DNAbin Manipulate DNA Sequences in Bit-Level Format
c.multiPhylo Building Lists of Trees
c.phylo Building Lists of Trees
CADM Congruence among distance matrices
CADM.global Congruence among distance matrices
CADM.post Congruence among distance matrices
carnivora Carnivora body sizes and life history traits
cbind.AAbin Amino Acid Sequences
cbind.DNAbin Manipulate DNA Sequences in Bit-Level Format
checkAlignment Check DNA Alignments
checkLabel Checking Labels
checkValidPhylo Check the Structure of a "phylo" Object
cherry Number of Cherries and Null Models of Trees
chiroptera Bat Phylogeny
chronoMPL Molecular Dating With Mean Path Lengths
chronopl Molecular Dating With Penalized Likelihood
chronos Molecular Dating by Penalised Likelihood and Maximum Likelihood
chronos.control Molecular Dating by Penalised Likelihood and Maximum Likelihood
cladewise Internal Reordering of Trees
clustal Multiple Sequence Alignment with External Applications
clustalomega Multiple Sequence Alignment with External Applications
coalescent.intervals Coalescent Intervals
coalescent.intervals.default Coalescent Intervals
coalescent.intervals.phylo 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
comparePhylo Compare Two "phylo" Objects
complement Translation from DNA to Amino Acid Sequences
compute.brlen Branch Lengths Computation
compute.brtime Compute and Set Branching Times
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
corphylo Correlations among Multiple Traits with Phylogenetic Signal
correlogram.formula Phylogenetic Correlogram
countBipartitions Split Frequencies and Conversion Among Split Classes
cynipids NEXUS Data Example

-- D --

data.nex NEXUS Data Example
dbd Probability Density Under Birth-Death Models
dbdTime Probability Density Under Birth-Death Models
def Definition of Vectors for Plotting or Annotating
del.colgapsonly Delete Alignment Gaps in DNA Sequences
del.gaps Delete Alignment Gaps in DNA Sequences
del.rowgapsonly Delete Alignment Gaps in DNA Sequences
delta.plot Delta Plots
deviance.ace Ancestral Character Estimation
di2multi Collapse and Resolve Multichotomies
di2multi.multiPhylo Collapse and Resolve Multichotomies
di2multi.phylo Collapse and Resolve Multichotomies
dist.aa Amino Acid Sequences
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
diversity.contrast.test Diversity Contrast Test
DNAbin Manipulate DNA Sequences in Bit-Level Format
DNAbin2indel Recode Blocks of Indels
dnds dN/dS Ratio
drawSupportOnEdges Extra Fuctions to Plot and Annotate Phylogenies
drop.fossil Tree Simulation Under the Time-Dependent Birth-Death Models
drop.tip Remove Tips in a Phylogenetic Tree
drop1.compar.gee Comparative Analysis with GEEs
dyule Probability Density Under Birth-Death Models

-- E --

edgelabels Labelling the Nodes, Tips, and Edges of a Tree
edges Draw Additional Edges on a Plotted Tree
editFileExtensions Tools to Explore Files
estimate.dates node.dating
estimate.mu node.dating
evonet Evolutionary Networks
ewLasso Incomplete distances and edge weights of unrooted topology
extract.clade Remove Tips in a Phylogenetic Tree
extract.popsize Reversible Jump MCMC to Infer Demographic History

-- F --

fancyarrows Draw Additional Edges on a Plotted Tree
FastME Tree Estimation Based on the Minimum Evolution Algorithm
fastme Tree Estimation Based on the Minimum Evolution Algorithm
fastme.bal Tree Estimation Based on the Minimum Evolution Algorithm
fastme.ols Tree Estimation Based on the Minimum Evolution Algorithm
find.skyline.epsilon Skyline Plot Estimate of Effective Population Size
Ftab Base frequencies from DNA Sequences

-- G --

gammaStat Gamma-Statistic of Pybus and Harvey
GC.content Base frequencies from DNA Sequences
getAnnotationsGenBank Read Annotations from GenBank
getMRCA Find Most Recent Common Ancestors Between Pairs
gopher.D Test of host-parasite coevolution

-- H --

has.singles Collapse Single Nodes
hivtree Phylogenetic Tree of 193 HIV-1 Sequences
hivtree.newick Phylogenetic Tree of 193 HIV-1 Sequences
hivtree.table Phylogenetic Tree of 193 HIV-1 Sequences
howmanytrees Calculate Numbers of Phylogenetic Trees
HP.links Test of host-parasite coevolution

-- I --

identify.phylo Graphical Identification of Nodes and Tips
image.AAbin Amino Acid Sequences
image.DNAbin Plot of DNA Sequence Alignement
Initialize.corPhyl Initialize a 'corPhyl' Structure Object
is.binary Test for Binary Tree
is.binary.multiPhylo Test for Binary Tree
is.binary.phylo Test for Binary Tree
is.binary.tree Test for Binary Tree
is.compatible Check Compatibility of Splits
is.compatible.bitsplits Check Compatibility of Splits
is.monophyletic Is Group Monophyletic
is.rooted Roots Phylogenetic Trees
is.rooted.multiPhylo Roots Phylogenetic Trees
is.rooted.phylo Roots Phylogenetic Trees
is.ultrametric Test if a Tree is Ultrametric
is.ultrametric.multiPhylo Test if a Tree is Ultrametric
is.ultrametric.phylo Test if a Tree is Ultrametric

-- K --

keep.tip Remove Tips in a Phylogenetic Tree
kronoviz Plot Multiple Chronograms on the Same Scale

-- L --

label2table Label Management
labels.AAbin Amino Acid Sequences
labels.DNAbin Manipulate DNA Sequences in Bit-Level Format
ladderize Ladderize a Tree
LargeNumber Calculate Numbers of Phylogenetic Trees
latag2n Leading and Trailing Alignment Gaps to N
lice.D Test of host-parasite coevolution
lines.popsize Reversible Jump MCMC to Infer Demographic History
lines.skyline Drawing Skyline Plot Graphs
lmorigin Multiple regression through the origin
lmorigin.ex1 Multiple regression through the origin
lmorigin.ex2 Multiple regression through the origin
logLik.ace Ancestral Character Estimation
LTT Theoretical Lineage-Through Time Plots
ltt.coplot Lineages Through Time Plot
ltt.lines Lineages Through Time Plot
ltt.plot Lineages Through Time Plot
ltt.plot.coords Lineages Through Time Plot

-- M --

makeChronosCalib Molecular Dating by Penalised Likelihood and Maximum Likelihood
makeLabel Label Management
makeLabel.character Label Management
makeLabel.DNAbin Label Management
makeLabel.multiPhylo Label Management
makeLabel.phylo 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
matching Conversion Between Phylo and Matching Objects
matexpo Matrix Exponential
mcconwaysims.test McConway-Sims Test of Homogeneous Diversification
mcmc.popsize Reversible Jump MCMC to Infer Demographic History
mixedFontLabel Mixed Font Labels for Plotting
mltt.plot Lineages Through Time Plot
Moran.I Moran's I Autocorrelation Index
MPR Most Parsimonious Reconstruction
mrca Find Most Recent Common Ancestors Between Pairs
mst Minimum Spanning Tree
multi2di Collapse and Resolve Multichotomies
multi2di.multiPhylo Collapse and Resolve Multichotomies
multi2di.phylo Collapse and Resolve Multichotomies
multiphylo Manipulating Lists of Trees
muscle Multiple Sequence Alignment with External Applications
mvr Minimum Variance Reduction
mvrs Minimum Variance Reduction

-- N --

Nedge Print Summary of a Phylogeny
Nedge.evonet Evolutionary Networks
Nedge.multiPhylo Print Summary of a Phylogeny
Nedge.phylo Print Summary of a Phylogeny
new2old.phylo Conversion Among Tree and Network Objects
nexus2DNAbin Read Character Data In NEXUS Format
nj Neighbor-Joining Tree Estimation
njs Tree Reconstruction from Incomplete Distances With NJ* or bio-NJ*
Nnode Print Summary of a Phylogeny
Nnode.multiPhylo Print Summary of a Phylogeny
Nnode.phylo Print Summary of a Phylogeny
node.dating node.dating
node.depth Depth and Heights of Nodes and Tips
node.depth.edgelength Depth and Heights of Nodes and Tips
node.height Depth and Heights of Nodes and Tips
nodelabels Labelling the Nodes, Tips, and Edges of a Tree
nodepath Find Paths of Nodes
Ntip Print Summary of a Phylogeny
Ntip.multiPhylo Print Summary of a Phylogeny
Ntip.phylo Print Summary of a Phylogeny

-- O --

old2new.phylo Conversion Among Tree and Network Objects

-- P --

parafit Test of host-parasite coevolution
pcoa Principal Coordinate Analysis
phydataplot Tree Annotation
phylo Read Tree File in Parenthetic Format
phymltest Fits a Bunch of Models with PhyML
pic Phylogenetically Independent Contrasts
pic.ortho Phylogenetically Independent Orthonormal Contrasts
plot.correlogram Plot a Correlogram
plot.correlogramList Plot a Correlogram
plot.evonet Evolutionary Networks
plot.mst Minimum Spanning Tree
plot.multiPhylo Plot Phylogenies
plot.phylo Plot Phylogenies
plot.phylo.extra Extra Fuctions to Plot and Annotate 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
plotBreakLongEdges Extra Fuctions to Plot and Annotate Phylogenies
plotTreeTime Plot Tree With Time Axis
postorder Internal Reordering of Trees
predict.compar.gee Comparative Analysis with GEEs
print.AAbin Amino Acid Sequences
print.ace Ancestral Character Estimation
print.binaryPGLMM Phylogenetic Generalized Linear Mixed Model for Binary Data
print.birthdeath Estimation of Speciation and Extinction Rates With Birth-Death Models
print.bitsplits Split Frequencies and Conversion Among Split Classes
print.chronos Molecular Dating by Penalised Likelihood and Maximum Likelihood
print.compar.gee Comparative Analysis with GEEs
print.comparePhylo Compare Two "phylo" Objects
print.corphylo Correlations among Multiple Traits with Phylogenetic Signal
print.DNAbin Manipulate DNA Sequences in Bit-Level Format
print.evonet Evolutionary Networks
print.LargeNumber Calculate Numbers of Phylogenetic Trees
print.lmorigin Multiple regression through the origin
print.multiPhylo Compact Display of a Phylogeny
print.parafit Test of host-parasite coevolution
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 --

rbdtree Tree Simulation Under the Time-Dependent Birth-Death Models
rbind.AAbin Amino Acid Sequences
rbind.DNAbin Manipulate DNA Sequences in Bit-Level Format
rcoal Generate Random Trees
rDNAbin Random DNA Sequences
read.caic Read Tree File in CAIC Format
read.dna Read DNA Sequences in a File
read.evonet Evolutionary Networks
read.FASTA Read DNA Sequences in a File
read.fastq Read DNA Sequences in a File
read.GenBank Read DNA Sequences from GenBank via Internet
read.gff Read GFF Files
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
reconstruct Continuous Ancestral Character Estimation
reorder.evonet Evolutionary Networks
reorder.multiPhylo Internal Reordering of Trees
reorder.phylo Internal Reordering of Trees
richness.yule.test Test of Diversification-Shift With the Yule Process
ring Tree Annotation
rlineage Tree Simulation Under the Time-Dependent Birth-Death Models
rmtopology Generate Random Trees
rmtree Generate Random Trees
root Roots Phylogenetic Trees
root.multiPhylo Roots Phylogenetic Trees
root.phylo Roots Phylogenetic Trees
rotate Swapping Sister Clades
rotateConstr Swapping Sister Clades
rphylo Tree Simulation Under the Time-Dependent Birth-Death Models
rtopology Generate Random Trees
rTraitCont Continuous Character Simulation
rTraitDisc Discrete Character Simulation
rTraitMult Multivariate Character Simulation
rtree Generate Random Trees
rtt Root a Tree by Root-to-Tip Regression

-- S --

SDM Construction of Consensus Distance Matrix With SDM
seg.sites Find Segregating Sites in DNA Sequences
skyline Skyline Plot Estimate of Effective Population Size
skyline.coalescentIntervals Skyline Plot Estimate of Effective Population Size
skyline.collapsedIntervals Skyline Plot Estimate of Effective Population Size
skyline.phylo Skyline Plot Estimate of Effective Population Size
skylineplot Drawing Skyline Plot Graphs
skylineplot.deluxe Drawing Skyline Plot Graphs
slowinskiguyer.test Slowinski-Guyer Test of Homogeneous Diversification
sort.bitsplits Split Frequencies and Conversion Among Split Classes
speciesTree Species Tree Estimation
str.multiPhylo Compact Display of a Phylogeny
stree Generates Systematic Regular Trees
stripLabel Label Management
subtreeplot Zoom on a Portion of a Phylogeny by Successive Clicks
subtrees All subtrees of a Phylogenetic Tree
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 --

tcoffee Multiple Sequence Alignment with External Applications
tiplabels Labelling the Nodes, Tips, and Edges of a Tree
trans Translation from DNA to Amino Acid Sequences
treePop Tree Popping
trex Tree Explorer With Multiple Devices
triangMtd Tree Reconstruction Based on the Triangles Method
triangMtds Tree Reconstruction Based on the Triangles Method

-- U --

ultrametric Incomplete Distance Matrix Filling
unique.multiPhylo Revomes Duplicate Trees
unroot Roots Phylogenetic Trees
unroot.multiPhylo Roots Phylogenetic Trees
unroot.phylo Roots Phylogenetic Trees
updateLabel Update Labels
updateLabel.AAbin Update Labels
updateLabel.character Update Labels
updateLabel.data.frame Update Labels
updateLabel.DNAbin Update Labels
updateLabel.evonet Update Labels
updateLabel.matrix Update Labels
updateLabel.phylo Update Labels

-- V --

varcomp Compute Variance Component Estimates
varCompPhylip Variance Components with Orthonormal Contrasts
vcv Phylogenetic Variance-covariance or Correlation Matrix
vcv.corPhyl Phylogenetic Variance-covariance or Correlation Matrix
vcv.phylo Phylogenetic Variance-covariance or Correlation Matrix
vcv2phylo Variance-Covariance Matrix to Tree

-- W --

weight.taxo Define Similarity Matrix
weight.taxo2 Define Similarity Matrix
where Find Patterns in DNA Sequences
which.edge Identifies Edges of a Tree
woodmouse Cytochrome b Gene Sequences of Woodmice
write.dna Write DNA Sequences in a File
write.evonet Evolutionary Networks
write.FASTA 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

-- X --

Xplor Tools to Explore Files
Xplorefiles Tools to Explore Files

-- Y --

yule Fits the 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 --

$.multiPhylo Manipulating Lists of Trees
$<-.multiPhylo Manipulating Lists of Trees
+.phylo Binds Trees
.compressTipLabel Building Lists of Trees
.uncompressTipLabel Building Lists of Trees
[.AAbin Amino Acid Sequences
[.DNAbin Manipulate DNA Sequences in Bit-Level Format
[.multiPhylo Manipulating Lists of Trees
[<-.multiPhylo Manipulating Lists of Trees
[[.multiPhylo Manipulating Lists of Trees
[[<-.multiPhylo Manipulating Lists of Trees