ape: Analyses of Phylogenetics and Evolution
Version 4.1

Functions for reading, writing, plotting, and manipulating phylogenetic trees, analyses of comparative data in a phylogenetic framework, ancestral character analyses, analyses of diversification and macroevolution, computing distances from DNA sequences, reading and writing nucleotide sequences as well as importing from BioConductor, and several tools such as Mantel's test, generalized skyline plots, graphical exploration of phylogenetic data (alex, trex, kronoviz), estimation of absolute evolutionary rates and clock-like trees using mean path lengths and penalized likelihood, dating trees with non-contemporaneous sequences, translating DNA into AA sequences, and assessing sequence alignments. Phylogeny estimation can be done with the NJ, BIONJ, ME, MVR, SDM, and triangle methods, and several methods handling incomplete distance matrices (NJ*, BIONJ*, MVR*, and the corresponding triangle method). Some functions call external applications (PhyML, Clustal, T-Coffee, Muscle) whose results are returned into R.

Browse man pages Browse package API and functions Browse package files

AuthorEmmanuel Paradis [aut, cre, cph], Simon Blomberg [aut, cph], Ben Bolker [aut, cph], Julien Claude [aut, cph], Hoa Sien Cuong [aut, cph], Richard Desper [aut, cph], Gilles Didier [aut, cph], Benoit Durand [aut, cph], Julien Dutheil [aut, cph], RJ Ewing [aut, cph], Olivier Gascuel [aut, cph], Christoph Heibl [aut, cph], Anthony Ives [aut, cph], Bradley Jones [aut, cph], Daniel Lawson [aut, cph], Vincent Lefort [aut, cph], Pierre Legendre [aut, cph], Jim Lemon [aut, cph], Rosemary McCloskey [aut, cph], Johan Nylander [aut, cph], Rainer Opgen-Rhein [aut, cph], Andrei-Alin Popescu [aut, cph], Manuela Royer-Carenzi [aut, cph], Klaus Schliep [aut, cph], Korbinian Strimmer [aut, cph], Damien de Vienne [aut, cph]
Date of publication2017-02-14 19:15:21
MaintainerEmmanuel Paradis <Emmanuel.Paradis@ird.fr>
LicenseGPL (>= 2)
Version4.1
URL http://ape-package.ird.fr/
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("ape")

Man pages

AAbin: Amino Acid Sequences
ace: Ancestral Character Estimation
additive: Incomplete Distance Matrix Filling
add.scale.bar: Add a Scale Bar to a Phylogeny Plot
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
ape-internal: Internal Ape Functions
ape-package: Analyses of Phylogenetics and Evolution
apetools: Tools to Explore Files
as.alignment: Conversion Among DNA Sequence Internal Formats
as.bitsplits: Split Frequencies and Conversion Among Split Classes
as.matching: Conversion Between Phylo and Matching Objects
as.phylo: Conversion Among Tree and Network Objects
as.phylo.formula: Conversion from Taxonomy Variables to Phylogenetic Trees
axisPhylo: Axis on Side of Phylogeny
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...
bd.time: Time-Dependent Birth-Death Models
binaryPGLMM: Phylogenetic Generalized Linear Mixed Model for Binary Data
bind.tree: Binds Trees
bionj: Tree Estimation Based on an Improved Version of the NJ...
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...
boot.phylo: Tree Bipartition and Bootstrapping Phylogenies
branching.times: Branching Times of a Phylogenetic Tree
CADM.global: Congruence among distance matrices
carnivora: Carnivora body sizes and life history traits
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...
clustal: Multiple Sequence Alignment with External Applications
coalescent.intervals: Coalescent Intervals
collapsed.intervals: Collapsed Coalescent Intervals
collapse.singles: Collapse Single Nodes
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
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...
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
corPagel: Pagel's "lambda" Correlation Structure
corphylo: Correlations among Multiple Traits with Phylogenetic Signal
correlogram.formula: Phylogenetic Correlogram
c.phylo: Building Lists of Trees
cynipids: NEXUS Data Example
dbd: Probability Density Under Birth-Death Models
def: Definition of Vectors for Plotting or Annotating
del.gaps: Delete Alignment Gaps in DNA Sequences
delta.plot: Delta Plots
dist.dna: Pairwise Distances from DNA Sequences
dist.gene: Pairwise Distances from Genetic Data
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
drop.tip: Remove Tips in a Phylogenetic Tree
edges: Draw Additional Edges on a Plotted Tree
evonet: Evolutionary Networks
ewLasso: Incomplete distances and edge weights of unrooted topology
fastme: Tree Estimation Based on the Minimum Evolution Algorithm
gammaStat: Gamma-Statistic of Pybus and Harvey
hivtree: Phylogenetic Tree of 193 HIV-1 Sequences
howmanytrees: Calculate Numbers of Phylogenetic Trees
identify.phylo: Graphical Identification of Nodes and Tips
image.DNAbin: Plot of DNA Sequence Alignement
Initialize.corPhyl: Initialize a 'corPhyl' Structure Object
is.binary.tree: Test for Binary Tree
is.compatible: Check Compatibility of Splits
is.monophyletic: Is Group Monophyletic
is.ultrametric: Test if a Tree is Ultrametric
kronoviz: Plot Multiple Chronograms on the Same Scale
label2table: Label Management
ladderize: Ladderize a Tree
lmorigin: Multiple regression through the origin
LTT: Theoretical Lineage-Through Time Plots
ltt.plot: Lineages Through Time Plot
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
mcconwaysims.test: McConway-Sims Test of Homogeneous Diversification
mcmc.popsize: Reversible Jump MCMC to Infer Demographic History
mixedFontLabel: Mixed Font Labels for Plotting
MoranI: 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
multiphylo: Manipulating Lists of Trees
mvr: Minimum Variance Reduction
nj: Neighbor-Joining Tree Estimation
njs: Tree Reconstruction from Incomplete Distances With NJ* or...
node.dating: node.dating
node.depth: Depth and Heights of Nodes and Tips
nodelabels: Labelling the Nodes, Tips, and Edges of a Tree
nodepath: Find Paths of Nodes
parafit: Test of host-parasite coevolution
pcoa: Principal Coordinate Analysis
phydataplot: Tree Annotation
phymltest: Fits a Bunch of Models with PhyML
pic: Phylogenetically Independent Contrasts
pic.ortho: Phylogenetically Independent Orthonormal Contrasts
plot.correlogram: Plot a Correlogram
plot.phylo: Plot Phylogenies
plot.phyloExtra: Extra Fuctions to Plot and Annotate Phylogenies
plotTreeTime: Plot Tree With Time Axis
plot.varcomp: Plot Variance Components
print.phylo: Compact Display of a Phylogeny
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.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.phylo: Internal Reordering of Trees
richness.yule.test: Test of Diversification-Shift With the Yule Process
rlineage: Tree Simulation Under the Time-Dependent Birth-Death Models
root: Roots Phylogenetic Trees
rotate: Swapping Sister Clades
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
SDM: Construction of Consensus Distance Matrix With SDM
seg.sites: Find Segregating Sites in DNA Sequences
skyline: Skyline Plot Estimate of Effective Population Size
skylineplot: Drawing Skyline Plot Graphs
slowinskiguyer.test: Slowinski-Guyer Test of Homogeneous Diversification
speciesTree: Species Tree Estimation
stree: Generates Systematic Regular Trees
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
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
unique.multiPhylo: Revomes Duplicate Trees
varcomp: Compute Variance Component Estimates
varCompPhylip: Variance Components with Orthonormal Contrasts
vcv2phylo: Variance-Covariance Matrix to Tree
vcv.phylo: Phylogenetic Variance-covariance or Correlation Matrix
weight.taxo: 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
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
zoom: Zoom on a Portion of a Phylogeny

Functions

$.multiPhylo Man page
$<-.multiPhylo Man page
+.phylo Man page
.compressTipLabel Man page
.uncompressTipLabel Man page
AAbin Man page
AAsubst Man page Source code
AIC.ace Man page Source code
BOTHlabels Man page Source code
BaseProportion Man page
CADM Man page
CADM.global Man page
CADM.post Man page
CDF.birth.death Man page Source code
CDF.birth.death2 Source code
C_additive Man page
C_bionj Man page
C_bionjs Man page
C_ewLasso Man page
C_mvr Man page
C_mvrs Man page
C_nj Man page
C_njs Man page
C_pic Man page
C_rTraitCont Man page
C_treePop Man page
C_triangMtd Man page
C_triangMtds Man page
C_ultrametric Man page
C_where Man page
CountBipartitionsFromTrees Man page
DNAAlignment2DNAbinMatrix Source code
DNAString2DNAbin Source code
DNAStringSet2DNAbin Source code
DNAbin Man page
DNAbin2indel Man page Source code
DNAbin2indelblock Man page
FastME Man page
Ftab Man page Source code
GC.content Man page Source code
GlobalDeletionDNA Man page
HP.links Man page
Initialize.corPhyl Man page Source code
LTT Man page Source code
MPR Man page Source code
Moran.I Man page Source code
Nedge Man page Source code
Nedge.multiPhylo Man page Source code
Nedge.phylo Man page Source code
Nnode Man page Source code
Nnode.multiPhylo Man page Source code
Nnode.phylo Man page Source code
Ntip Man page Source code
Ntip.multiPhylo Man page Source code
Ntip.phylo Man page Source code
ONEwise Man page Source code
SDM Man page Source code
SegSites Man page
Xplorefiles Man page Source code
[.AAbin Man page
[.DNAbin Man page
[.multiPhylo Man page
[<-.multiPhylo Man page
[[.multiPhylo Man page
[[<-.multiPhylo Man page
abbreviateGenus Man page Source code
ace Man page Source code
add.scale.bar Man page Source code
additive Man page Source code
alex Man page Source code
all.equal.DNAbin Man page Source code
all.equal.phylo Man page Source code
alview Man page Source code
anova.ace Man page Source code
ape Man page
ape-package Man page
apetools Man page
arecompatible Man page Source code
as.AAbin Man page Source code
as.AAbin.character Man page Source code
as.DNAbin Man page Source code
as.DNAbin.DNAMultipleAlignment Man page Source code
as.DNAbin.DNAString Man page Source code
as.DNAbin.DNAStringSet Man page Source code
as.DNAbin.PairwiseAlignmentsSingleSubject Man page Source code
as.DNAbin.alignment Man page Source code
as.DNAbin.character Man page Source code
as.DNAbin.list Man page Source code
as.alignment Man page Source code
as.bitsplits Man page Source code
as.bitsplits.prop.part Man page Source code
as.character.AAbin Man page Source code
as.character.DNAbin Man page Source code
as.hclust.phylo Man page Source code
as.igraph Man page
as.igraph.evonet Man page Source code
as.igraph.phylo Man page Source code
as.list.DNAbin Man page Source code
as.matching Man page Source code
as.matching.phylo Man page Source code
as.matrix.DNAbin Man page Source code
as.network.evonet Man page Source code
as.network.phylo Man page Source code
as.networx.evonet Man page Source code
as.phyDat.AAbin Man page Source code
as.phylo Man page Source code
as.phylo.evonet Man page Source code
as.phylo.formula Man page Source code
as.phylo.hclust Man page Source code
as.phylo.matching Man page Source code
as.phylo.phylog Man page Source code
as.prop.part Man page Source code
as.prop.part.bitsplits Man page Source code
axisPhylo Man page Source code
balance Man page Source code
base.freq Man page Source code
bd.ext Man page Source code
bd.time Man page Source code
binaryPGLMM Man page Source code
binaryPGLMM.sim Man page Source code
bind.tree Man page Source code
bionj Man page Source code
bionjs Man page Source code
bipartition Man page
biplot.pcoa Man page
bird.families Man page
bird.orders Man page
birth.step Man page Source code
birthdeath Man page Source code
bitsplits Man page Source code
bitsplits_multiPhylo Man page
bitsplits_phylo Man page
boot.phylo Man page Source code
branching.times Man page Source code
bydir Man page Source code
c.DNAbin Man page Source code
c.multiPhylo Man page Source code
c.phylo Man page Source code
c_phylo_single Source code
calculeC Man page Source code
calculeC_ABM Man page Source code
calculeC_OU Man page Source code
carnivora Man page
cbind.DNAbin Man page Source code
checkAlignment Man page Source code
checkLabel Man page Source code
checkValidPhylo Man page Source code
cherry Man page Source code
chiroptera Man page
chronoMPL Man page Source code
chronopl Man page Source code
chronopl.cv Man page Source code
chronos Man page Source code
chronos.control Man page Source code
circular.plot Man page Source code
clado.build Man page Source code
cladogram.plot Man page Source code
clustal Man page Source code
clustalomega Man page Source code
coalescent.intervals Man page Source code
coalescent.intervals.default Man page Source code
coalescent.intervals.phylo Man page Source code
coef.corBlomberg Man page Source code
coef.corBrownian Man page Source code
coef.corGrafen Man page Source code
coef.corMartins Man page Source code
coef.corPagel Man page Source code
collapse.singles Man page Source code
collapsed.intervals Man page Source code
compar.cheverud Man page Source code
compar.gee Man page Source code
compar.lynch Man page Source code
compar.ou Man page Source code
complement Man page Source code
compressTipLabel Source code
compute.brlen Man page Source code
compute.brtime Man page Source code
consensus Man page Source code
cophenetic.phylo Man page Source code
cophyloplot Man page Source code
corBlomberg Man page Source code
corBrownian Man page Source code
corClasses Man page
corGrafen Man page Source code
corMartins Man page Source code
corMatrix.corBlomberg Man page Source code
corMatrix.corBrownian Man page Source code
corMatrix.corGrafen Man page Source code
corMatrix.corMartins Man page Source code
corMatrix.corPagel Man page Source code
corPagel Man page Source code
corPhyl Man page
corphylo Man page Source code
correlogram.formula Man page Source code
countBipartitions Man page Source code
cynipids Man page
data.nex Man page
dbd Man page Source code
dbdTime Man page Source code
death.step Man page Source code
def Man page Source code
del.colgapsonly Man page Source code
del.gaps Man page Source code
del.rowgapsonly Man page Source code
delta.plot Man page Source code
delta_plot Man page
deviance.ace Man page Source code
di2multi Man page Source code
di2multi.multiPhylo Man page Source code
di2multi.phylo Man page Source code
di2multi_ape Source code
dist.aa Man page Source code
dist.dna Man page Source code
dist.gene Man page Source code
dist.nodes Man page Source code
dist.topo Man page Source code Source code
dist_dna Man page
dist_nodes Man page
diversi.gof Man page Source code
diversi.time Man page Source code
diversity.contrast.test Man page Source code
drawSupportOnEdges Man page Source code
drop.fossil Man page Source code
drop.tip Man page Source code
drop1.compar.gee Man page Source code
dyule Man page Source code
edgelabels Man page Source code
edges Man page Source code
editFileExtensions Man page Source code
errorAlignment Source code
estimate.dates Man page Source code
estimate.mu Man page Source code
evonet Man page Source code
ewLasso Man page Source code
extract.clade Man page Source code
extract.popsize Man page Source code
f.cherry.uniform Man page Source code
f.cherry.yule Man page Source code
fancyarrows Man page Source code
fastme Man page
fastme.bal Man page Source code
fastme.ols Man page Source code
find.skyline.epsilon Man page Source code
floating.pie.asp Man page Source code
gammaStat Man page Source code
getCase Source code
getMLHessian Man page Source code
getMRCA Man page Source code
getREMLHessian Man page Source code
getRHOetINT Source code
getSEs Source code
getSeparatorTaxaLabels Source code
getSumSquare Man page Source code
getTreesFromDotdotdot Source code
glsABM Man page Source code
glsBM Man page Source code
glsOUv1 Man page Source code
glsOUv2 Man page Source code
gopher.D Man page
hivtree Man page
hivtree.newick Man page
hivtree.table Man page
howmanytrees Man page Source code
ht.move Man page Source code
identify.phylo Man page Source code
image.AAbin Man page Source code
image.DNAbin Man page Source code
integrateTrapeze Man page Source code
is.binary Man page Source code
is.binary.multiPhylo Man page Source code
is.binary.phylo Man page Source code
is.binary.tree Man page Source code
is.compatible Man page Source code
is.compatible.bitsplits Man page Source code
is.monophyletic Man page Source code
is.rooted Man page Source code
is.rooted.multiPhylo Man page Source code
is.rooted.phylo Man page Source code
is.ultrametric Man page Source code
is.ultrametric.multiPhylo Man page Source code
is.ultrametric.phylo Man page Source code
kronoviz Man page Source code
label2table Man page Source code
labels.AAbin Man page Source code
labels.DNAbin Man page Source code
ladderize Man page Source code
lice.D Man page
lines.popsize Man page Source code
lines.skyline Man page Source code
lmorigin Man page
lmorigin.ex1 Man page
lmorigin.ex2 Man page
logLik.ace Man page Source code
loglik.pop Man page Source code
lower.triang Man page Source code
ltt.coplot Man page Source code
ltt.lines Man page Source code
ltt.plot Man page Source code
ltt.plot.coords Man page Source code
makeChronosCalib Man page Source code
makeLabel Man page Source code
makeLabel.DNAbin Man page Source code
makeLabel.character Man page Source code
makeLabel.multiPhylo Man page Source code
makeLabel.phylo Man page Source code
makeMultiPhyloFromObj Source code
makeNodeLabel Man page Source code
makePhylo Source code
mant.zstat Man page Source code
mantel.test Man page Source code
mat3 Man page
mat5M3ID Man page
mat5Mrand Man page
mat_expo Man page
matchDataPhylo Source code
matching Man page
matexpo Man page Source code
mcconwaysims.test Man page Source code
mcmc.popsize Man page Source code
me_b Man page
me_o Man page
mixedFontLabel Man page Source code
mltt.plot Man page Source code
mrca Man page Source code
mst Man page Source code
multi2di Man page Source code
multi2di.multiPhylo Man page Source code
multi2di.phylo Man page Source code
multi2di_ape Source code
multiphylo Man page
muscle Man page Source code
mvr Man page Source code
mvrs Man page Source code
new2old.phylo Man page Source code
neworder_phylo Man page
neworder_pruningwise Man page
nj Man page Source code
njs Man page Source code
node.dating Man page
node.depth Man page Source code
node.depth.edgelength Man page Source code
node.height Man page Source code
node_depth Man page
node_depth_edgelength Man page
node_height Man page
node_height_clado Man page
nodelabels Man page Source code
nodepath Man page Source code
nsca Man page Source code
old2new.phylo Man page Source code
parafit Man page
pcoa Man page Source code
perm.rowscols Man page Source code
phydataplot Man page Source code
phylo Man page
phylogram.plot Man page Source code
phymltest Man page Source code
pic Man page Source code
pic.ortho Man page Source code
plot.correlogram Man page Source code
plot.correlogramList Man page Source code
plot.evonet Man page Source code
plot.mst Man page Source code
plot.multiPhylo Man page Source code
plot.phylo Man page Source code
plot.phylo.extra Man page
plot.phymltest Man page Source code
plot.popsize Man page Source code
plot.prop.part Man page Source code
plot.skyline Man page Source code
plot.varcomp Man page Source code
plotBreakLongEdges Man page Source code
plotCophylo2 Man page Source code
plotPhyloCoor Man page Source code
plotTreeTime Man page Source code
polar2rect Man page Source code
pos.move Man page Source code
postprocess.prop.part Man page Source code
predict.compar.gee Man page Source code
print.AAbin Man page Source code
print.DNAbin Man page Source code
print.ace Man page Source code
print.binaryPGLMM Man page Source code
print.birthdeath Man page Source code
print.bitsplits Man page Source code
print.chronos Man page Source code
print.compar.gee Man page Source code
print.corphylo Man page Source code
print.evonet Man page Source code
print.lmorigin Man page
print.multiPhylo Man page Source code
print.parafit Man page
print.phylo Man page Source code
print.phymltest Man page Source code
print.prop.part Man page Source code
prop.clades Man page Source code
prop.part Man page Source code
prop_part Man page
rTraitCont Man page Source code
rTraitDisc Man page Source code
rTraitMult Man page Source code
racine Man page Source code
rawStreamToDNAbin Man page
rbdtree Man page Source code
rbind.DNAbin Man page Source code
rcoal Man page Source code
read.FASTA Man page Source code
read.GenBank Man page Source code
read.caic Man page Source code
read.dna Man page Source code
read.fastq Man page Source code
read.gff Man page Source code
read.nexus Man page Source code
read.nexus.data Man page
read.tree Man page Source code
reconstruct Man page Source code
rect2polar Man page Source code
renumeroteArbre Man page Source code
reorder.multiPhylo Man page Source code
reorder.phylo Man page Source code
reorder_ape Source code
richness.yule.test Man page Source code
ring Man page Source code
rlineage Man page Source code
rmtree Man page Source code
root Man page Source code
root.multiPhylo Man page Source code
root.phylo Man page Source code
rotate Man page Source code
rotateConstr Man page Source code
rphylo Man page Source code
rtree Man page Source code
rtt Man page Source code
s.rooted_ape Source code
s.ultrametric_ape Source code
seg.sites Man page Source code
seq_root2tip Man page
skyline Man page Source code
skyline.coalescentIntervals Man page Source code
skyline.collapsedIntervals Man page Source code
skyline.phylo Man page Source code
skylineplot Man page Source code
skylineplot.deluxe Man page Source code
slowinskiguyer.test Man page Source code
sort.bitsplits Man page Source code
sortIndex Man page Source code
speciesTree Man page Source code
str.multiPhylo Man page Source code
stree Man page Source code
stripLabel Man page Source code
subtreeplot Man page Source code
subtrees Man page Source code
summary.phylo Man page Source code
summary.phymltest Man page Source code
summary.prop.part Man page Source code
tcoffee Man page Source code
tiplabels Man page Source code
trans Man page Source code
trans_DNA2AA Man page
tree.build Man page Source code
treeBuildWithTokens Man page Source code
treePop Man page Source code
trex Man page Source code
triangMtd Man page Source code
triangMtds Man page Source code
ultrametric Man page Source code
uncompressTipLabel Source code
unique.multiPhylo Man page Source code
unroot Man page Source code
unroot.multiPhylo Man page Source code
unroot.phylo Man page Source code
unroot_ape Source code
unrooted.plot Man page
unrooted.xy Man page Source code
varCompPhylip Man page Source code
varcomp Man page Source code
vcv Man page Source code
vcv.corPhyl Man page Source code
vcv.phylo Man page Source code
vcv2phylo Man page Source code
weight.taxo Man page Source code
weight.taxo2 Man page Source code
where Man page Source code
which.edge Man page Source code
woodmouse Man page
write.dna Man page Source code
write.nexus Man page Source code
write.nexus.data Man page Source code
write.tree Man page Source code
write.tree2 Source code
yule Man page Source code
yule.cov Man page Source code
yule.time Man page Source code
zoom Man page Source code

Files

COPYING
inst
inst/CITATION
inst/doc
inst/doc/MoranI.pdf
inst/doc/MoranI.R
inst/doc/MoranI.Rnw
src
src/Makevars
src/NNI.c
src/TBR.c
src/pic.c
src/nj.c
src/bipartition.c
src/heap.c
src/delta_plot.c
src/tree_build.c
src/ewLasso.c
src/mvrs.c
src/bNNI.c
src/mvr.c
src/read_dna.c
src/me_ols.c
src/mat_expo.c
src/SPR.c
src/njs.c
src/additive.c
src/rTrait.c
src/bionjs.c
src/plot_phylo.c
src/treePop.c
src/bitsplits.c
src/dist_nodes.c
src/tree_phylo.c
src/me_balanced.c
src/reorder_phylo.c
src/me.h
src/dist_dna.c
src/BIONJ.c
src/triangMtds.c
src/triangMtd.c
src/ape.h
src/ultrametric.c
src/me.c
src/ape.c
NAMESPACE
NEWS
data
data/cynipids.rda
data/lmorigin.ex1.rda
data/bird.families.rda
data/carnivora.csv.gz
data/mat5M3ID.RData
data/chiroptera.rda
data/hivtree.table.txt.gz
data/bird.orders.rda
data/hivtree.newick.rda
data/lice.D.rda
data/lmorigin.ex2.rda
data/mat3.RData
data/gopher.D.rda
data/woodmouse.rda
data/HP.links.rda
data/mat5Mrand.RData
R
R/plot.phylo.R
R/biplot.pcoa.R
R/balance.R
R/read.dna.R
R/read.nexus.data.R
R/zoom.R
R/phymltest.R
R/is.binary.tree.R
R/is.monophyletic.R
R/ace.R
R/rtree.R
R/compute.brtime.R
R/dbd.R
R/me.R
R/Cheverud.R
R/skylineplot.R
R/def.R
R/compar.lynch.R
R/CDF.birth.death.R
R/gammaStat.R
R/chronopl.R
R/cophyloplot.R
R/apetools.R
R/corphylo.R
R/dist.gene.R
R/cophenetic.phylo.R
R/makeNodeLabel.R
R/diversi.gof.R
R/treePop.R
R/lmorigin.R
R/MPR.R
R/CADM.global.R
R/speciesTree.R
R/read.tree.R
R/drop.tip.R
R/read.gff.R
R/ewLasso.R
R/DNA.R
R/identify.phylo.R
R/binaryPGLMM.R
R/delta.plot.R
R/vcv2phylo.R
R/mrca.R
R/node.dating.R
R/write.nexus.data.R
R/compar.gee.R
R/cherry.R
R/as.phylo.formula.R
R/howmanytrees.R
R/as.phylo.R
R/summary.phylo.R
R/birthdeath.R
R/subtreeplot.R
R/nodepath.R
R/all.equal.phylo.R
R/which.edge.R
R/MoranI.R
R/evonet.R
R/nj.R
R/is.compatible.R
R/mvr.R
R/rTrait.R
R/ltt.plot.R
R/collapsed.intervals.R
R/rotate.R
R/extract.popsize.R
R/skyline.R
R/makeLabel.R
R/matexpo.R
R/parafit.R
R/pcoa.R
R/write.nexus.R
R/print.parafit.R
R/yule.R
R/as.bitsplits.R
R/mst.R
R/checkValidPhylo.R
R/yule.time.R
R/branching.times.R
R/compar.ou.R
R/plot.popsize.R
R/clustal.R
R/root.R
R/write.dna.R
R/collapse.singles.R
R/read.GenBank.R
R/triangMtd.R
R/rtt.R
R/pic.R
R/CADM.post.R
R/print.lmorigin.R
R/reconstruct.R
R/ladderize.R
R/subtrees.R
R/mcmc.popsize.R
R/bind.tree.R
R/chronoMPL.R
R/is.ultrametric.R
R/read.nexus.R
R/nodelabels.R
R/vcv.phylo.R
R/phydataplot.R
R/varcomp.R
R/chronos.R
R/mantel.test.R
R/multi2di.R
R/unique.multiPhylo.R
R/plot.phyloExtra.R
R/additive.R
R/coalescent.intervals.R
R/alex.R
R/plotPhyloCoor.R
R/PGLS.R
R/diversi.time.R
R/njs.R
R/dist.topo.R
R/write.tree.R
R/as.matching.R
R/SDM.R
R/SlowinskiGuyer.R
R/zzz.R
R/scales.R
R/reorder.phylo.R
R/read.caic.R
vignettes
vignettes/ape.bib
vignettes/MoranI.Rnw
MD5
build
build/vignette.rds
DESCRIPTION
man
man/makeLabel.Rd
man/bd.ext.Rd
man/makeNodeLabel.Rd
man/read.dna.Rd
man/mcconwaysims.test.Rd
man/binaryPGLMM.Rd
man/compute.brlen.Rd
man/ewLasso.Rd
man/pic.ortho.Rd
man/plot.correlogram.Rd
man/add.scale.bar.Rd
man/richness.yule.test.Rd
man/multi2di.Rd
man/trex.Rd
man/mantel.test.Rd
man/edges.Rd
man/rTraitDisc.Rd
man/varcomp.Rd
man/mat5Mrand.Rd
man/nodelabels.Rd
man/checkAlignment.Rd
man/varCompPhylip.Rd
man/compar.gee.Rd
man/del.gaps.Rd
man/pic.Rd
man/where.Rd
man/unique.multiPhylo.Rd
man/is.compatible.Rd
man/SDM.Rd
man/bird.orders.Rd
man/plot.phyloExtra.Rd
man/triangMtd.Rd
man/ape-package.Rd
man/MoranI.Rd
man/chronoMPL.Rd
man/AAbin.Rd
man/howmanytrees.Rd
man/cophyloplot.Rd
man/dbd.Rd
man/chronopl.Rd
man/read.GenBank.Rd
man/LTT.Rd
man/c.phylo.Rd
man/DNAbin.Rd
man/hivtree.Rd
man/as.bitsplits.Rd
man/corBlomberg.Rd
man/mat3.Rd
man/dist.dna.Rd
man/compar.lynch.Rd
man/stree.Rd
man/read.tree.Rd
man/weight.taxo.Rd
man/subtrees.Rd
man/reorder.phylo.Rd
man/kronoviz.Rd
man/read.nexus.Rd
man/def.Rd
man/rtt.Rd
man/phymltest.Rd
man/yule.cov.Rd
man/speciesTree.Rd
man/boot.phylo.Rd
man/rTraitMult.Rd
man/rotate.Rd
man/skyline.Rd
man/skylineplot.Rd
man/is.monophyletic.Rd
man/all.equal.phylo.Rd
man/axisPhylo.Rd
man/corPagel.Rd
man/print.phylo.Rd
man/plot.varcomp.Rd
man/dist.gene.Rd
man/write.dna.Rd
man/compute.brtime.Rd
man/is.binary.tree.Rd
man/branching.times.Rd
man/apetools.Rd
man/additive.Rd
man/corClasses.Rd
man/bind.tree.Rd
man/bird.families.Rd
man/alex.Rd
man/corBrownian.Rd
man/rTraitCont.Rd
man/is.ultrametric.Rd
man/chronos.Rd
man/compar.cheverud.Rd
man/MPR.Rd
man/mat5M3ID.Rd
man/as.matching.Rd
man/correlogram.formula.Rd
man/njs.Rd
man/write.tree.Rd
man/root.Rd
man/bd.time.Rd
man/corphylo.Rd
man/birthdeath.Rd
man/compar.ou.Rd
man/multiphylo.Rd
man/summary.phylo.Rd
man/alview.Rd
man/diversi.gof.Rd
man/mvr.Rd
man/consensus.Rd
man/matexpo.Rd
man/diversi.time.Rd
man/as.alignment.Rd
man/which.edge.Rd
man/rtree.Rd
man/identify.phylo.Rd
man/mixedFontLabel.Rd
man/zoom.Rd
man/corGrafen.Rd
man/DNAbin2indel.Rd
man/trans.Rd
man/write.nexus.data.Rd
man/carnivora.Rd
man/vcv.phylo.Rd
man/subtreeplot.Rd
man/node.dating.Rd
man/corMartins.Rd
man/clustal.Rd
man/read.gff.Rd
man/nj.Rd
man/node.depth.Rd
man/vcv2phylo.Rd
man/phydataplot.Rd
man/rlineage.Rd
man/yule.Rd
man/write.nexus.Rd
man/Initialize.corPhyl.Rd
man/evonet.Rd
man/yule.time.Rd
man/diversity.contrast.test.Rd
man/slowinskiguyer.test.Rd
man/chiroptera.Rd
man/as.phylo.Rd
man/lmorigin.Rd
man/ltt.plot.Rd
man/dist.topo.Rd
man/bionj.Rd
man/read.caic.Rd
man/image.DNAbin.Rd
man/reconstruct.Rd
man/mst.Rd
man/treePop.Rd
man/all.equal.DNAbin.Rd
man/fastme.Rd
man/collapsed.intervals.Rd
man/mrca.Rd
man/as.phylo.formula.Rd
man/read.nexus.data.Rd
man/nodepath.Rd
man/collapse.singles.Rd
man/balance.Rd
man/woodmouse.Rd
man/ladderize.Rd
man/cherry.Rd
man/CADM.global.Rd
man/base.freq.Rd
man/delta.plot.Rd
man/ace.Rd
man/parafit.Rd
man/plotTreeTime.Rd
man/pcoa.Rd
man/seg.sites.Rd
man/cynipids.Rd
man/gammaStat.Rd
man/cophenetic.phylo.Rd
man/ape-internal.Rd
man/plot.phylo.Rd
man/drop.tip.Rd
man/coalescent.intervals.Rd
man/checkValidPhylo.Rd
man/mcmc.popsize.Rd
man/label2table.Rd
ape documentation built on May 20, 2017, 3:54 a.m.