ape: Analyses of Phylogenetics and Evolution

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.

Install the latest version of this package by entering the following in R:
install.packages("ape")
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
http://ape-package.ird.fr/

View on CRAN

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

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

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

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