Analyses of Phylogenetics and Evolution

---

Documentation for package ‘ape’ version 5.8

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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.default	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
degree	Vertex Degrees in Trees and Networks
degree.evonet	Vertex Degrees in Trees and Networks
degree.phylo	Vertex Degrees in Trees and Networks
del.colgapsonly	Delete Alignment Gaps in DNA or AA Sequences
del.gaps	Delete Alignment Gaps in DNA or AA Sequences
del.rowgapsonly	Delete Alignment Gaps in DNA or AA 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
drop.tip.multiPhylo	Remove Tips in a Phylogenetic Tree
drop.tip.phylo	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
efastats	Multiple Sequence Alignment with External Applications
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
keep.tip.multiPhylo	Remove Tips in a Phylogenetic Tree
keep.tip.phylo	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
letterconf	Multiple Sequence Alignment with External Applications
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
makeNodeLabel.multiPhylo	Makes Node Labels
makeNodeLabel.phylo	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
muscle5	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
solveAmbiguousBases	Solve Ambiguous Bases in DNA Sequences
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