# Analyses of Phylogenetics and Evolution

## Documentation for package ‘ape’ version 4.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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.character | 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.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.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.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.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.DNAbin | Manipulate DNA Sequences in Bit-Level Format
checkAlignment | Check DNA Alignments
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
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
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
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
getMRCA | Find Most Recent Common Ancestors Between Pairs
gopher.D | Test of host-parasite coevolution

## -- H --

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 --

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
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.multiPhylo | Print Summary of a Phylogeny
Nedge.phylo | Print Summary of a Phylogeny
new2old.phylo | Conversion Among Tree and Network Objects
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
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.corphylo | Correlations among Multiple Traits with Phylogenetic Signal
print.DNAbin | Manipulate DNA Sequences in Bit-Level Format
print.evonet | Evolutionary Networks
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.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.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.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
rmtree | Generates 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
rTraitCont | Continuous Character Simulation
rTraitDisc | Discrete Character Simulation
rTraitMult | Multivariate Character Simulation
rtree | Generates 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

## -- 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.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 --

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