ape-package	ape-package
$.multiPhylo	print.phylo
+.phylo	bind.tree
ace	ace
add.scale.bar	add.scale.bar
AIC.ace	ace
all.equal.phylo	all.equal.phylo
anova.ace	ace
ape	ape-package
as.alignment	as.alignment
as.character.DNAbin	as.alignment
as.DNAbin	as.alignment
as.DNAbin.alignment	as.alignment
as.DNAbin.character	as.alignment
as.DNAbin.list	as.alignment
as.hclust.phylo	as.phylo
as.matching	as.matching
as.matching.phylo	as.matching
as.matrix.DNAbin	DNAbin
as.phylo	as.phylo
as.phylo.formula	as.phylo.formula
as.phylo.hclust	as.phylo
as.phylo.matching	as.matching
as.phylo.phylog	as.phylo
axisPhylo	axisPhylo
balance	balance
base.freq	base.freq
bd.ext	bd.ext
bind.tree	bind.tree
bionj	bionj
biplot.pcoa	pcoa
bird.families	bird.families
bird.orders	bird.orders
birth.step	ape-internal
birthdeath	birthdeath
boot.phylo	boot.phylo
BOTHlabels	ape-internal
branching.times	branching.times
c.DNAbin	DNAbin
CADM	CADM.global
CADM.global	CADM.global
CADM.post	CADM.global
carnivora	carnivora
cbind.DNAbin	DNAbin
checkLabel	ape-internal
cherry	cherry
chiroptera	chiroptera
chronogram	chronogram
chronoMPL	chronoMPL
chronopl	chronopl
chronopl.cv	ape-internal
circular.plot	ape-internal
clado.build	ape-internal
cladogram.plot	ape-internal
coalescent.intervals	coalescent.intervals
coalescent.intervals.default	coalescent.intervals
coalescent.intervals.phylo	coalescent.intervals
coef.corBlomberg	corBlomberg
coef.corBrownian	corBrownian
coef.corGrafen	corGrafen
coef.corMartins	corMartins
coef.corPagel	corPagel
collapse.singles	collapse.singles
collapsed.intervals	collapsed.intervals
compar.cheverud	compar.cheverud
compar.gee	compar.gee
compar.lynch	compar.lynch
compar.ou	compar.ou
compute.brlen	compute.brlen
consensus	consensus
cophenetic.phylo	cophenetic.phylo
cophyloplot	cophyloplot
corBlomberg	corBlomberg
corBrownian	corBrownian
corClasses	corClasses
corGrafen	corGrafen
corMartins	corMartins
corMatrix.corBlomberg	corBlomberg
corMatrix.corBrownian	corBrownian
corMatrix.corGrafen	corGrafen
corMatrix.corMartins	corMartins
corMatrix.corPagel	corPagel
corPagel	corPagel
corPhyl	corClasses
correlogram.formula	correlogram.formula
cynipids	cynipids
data.nex	cynipids
death.step	ape-internal
del.gaps	del.gaps
delta.plot	delta.plot
deviance.ace	ace
di2multi	multi2di
dist.dna	dist.dna
dist.gene	dist.gene
dist.nodes	cophenetic.phylo
dist.topo	dist.topo
diversi.gof	diversi.gof
diversi.time	diversi.time
DNAbin	DNAbin
DNAmodel	ape-defunct
drop.tip	drop.tip
drop1.compar.gee	compar.gee
edgelabels	nodelabels
edges	edges
evolve.phylo	evolve.phylo
extract.clade	drop.tip
extract.popsize	mcmc.popsize
f.cherry.uniform	ape-internal
f.cherry.yule	ape-internal
fancyarrows	edges
fastme	fastme
fastme.bal	fastme
fastme.ols	fastme
find.skyline.epsilon	skyline
floating.pie.asp	ape-internal
gammaStat	gammaStat
GC.content	GC.content
getDurations	ape-internal
getEdgeLengths	ape-internal
getExternalParams	ape-internal
getMRCA	ape-internal
getNEdges	ape-internal
getNFreeParams	ape-internal
getRates	ape-internal
gopher.D	parafit
H	ape-defunct
heterozygosity	ape-defunct
hivtree	hivtree
hivtree.newick	hivtree
hivtree.table	hivtree
howmanytrees	howmanytrees
HP.links	parafit
ht.move	ape-internal
identify.phylo	identify.phylo
Initialize.corPhyl	Initialize.corPhyl
is.binary.tree	is.binary.tree
is.monophyletic	is.monophyletic
is.rooted	root
is.ultrametric	is.ultrametric
klastorin	ape-defunct
ladderize	ladderize
landplants	landplants
landplants.newick	landplants
lice.D	parafit
lines.popsize	mcmc.popsize
lines.skyline	skylineplot
lmorigin	lmorigin
lmorigin.ex1	lmorigin
lmorigin.ex2	lmorigin
logLik.ace	ace
loglik.pop	ape-internal
lower.triang	ape-internal
ltt.lines	ltt.plot
ltt.plot	ltt.plot
makeLabel	makeLabel
makeLabel.character	makeLabel
makeLabel.DNAbin	makeLabel
makeLabel.multiPhylo	makeLabel
makeLabel.phylo	makeLabel
makeNodeLabel	makeNodeLabel
mant.zstat	ape-internal
mantel.test	mantel.test
mat3	mat3
mat5M3ID	mat5M3ID
mat5Mrand	mat5Mrand
matexpo	matexpo
mcmc.popsize	mcmc.popsize
mlphylo	ape-defunct
mltt.plot	ltt.plot
Moran.I	MoranI
mrca	mrca
mst	mst
multi2di	multi2di
Nedge	summary.phylo
nEdges	ape-internal
new2old.phylo	as.phylo
nj	nj
Nnode	summary.phylo
nNodes	ape-internal
node.depth	node.depth
node.height	ape-internal
node.height.clado	ape-internal
nodelabels	nodelabels
NPRS.criterion	NPRS.criterion
nsca	ape-internal
Ntip	summary.phylo
nuc.div	ape-defunct
objFuncLogScale	ape-internal
old2new.phylo	as.phylo
opsin	opsin
opsin.newick	opsin
optimTree	ape-internal
parafit	parafit
pcoa	pcoa
perm.rowscols	ape-internal
phylogram	ape-internal
phylogram.plot	ape-internal
phymltest	phymltest
pic	pic
plot.ancestral	plot.ancestral
plot.correlogram	plot.correlogram
plot.correlogramList	plot.correlogram
plot.mst	mst
plot.multiPhylo	plot.phylo
plot.phylo	plot.phylo
plot.phymltest	phymltest
plot.popsize	mcmc.popsize
plot.prop.part	boot.phylo
plot.skyline	skylineplot
plot.varcomp	plot.varcomp
plotCophylo2	ape-internal
plotPhyloCoor	ape-internal
pos.move	ape-internal
prepareTree	ape-internal
print.birthdeath	birthdeath
print.compar.gee	compar.gee
print.DNAbin	DNAbin
print.lmorigin	lmorigin
print.multiPhylo	print.phylo
print.parafit	parafit
print.phylo	print.phylo
print.phymltest	phymltest
print.prop.part	boot.phylo
prop.clades	boot.phylo
prop.part	boot.phylo
ratogram	ratogram
rbind.DNAbin	DNAbin
rcoal	rtree
read.caic	read.caic
read.dna	read.dna
read.GenBank	read.GenBank
read.nexus	read.nexus
read.nexus.data	read.nexus.data
read.tree	read.tree
reorder.phylo	reorder.phylo
rmtree	rtree
root	root
rotate	rotate
rTraitCont	rTraitCont
rTraitDisc	rTraitDisc
rtree	rtree
seg.sites	seg.sites
setTree	ape-internal
sh.test	ape-defunct
skyline	skyline
skyline.coalescentIntervals	skyline
skyline.collapsedIntervals	skyline
skyline.phylo	skyline
skylineplot	skylineplot
skylineplot.deluxe	skylineplot
sortIndex	ape-internal
str.multiPhylo	print.phylo
stree	stree
subtreeplot	subtreeplot
subtrees	subtrees
summary.DNAbin	DNAbin
summary.phylo	summary.phylo
summary.phymltest	phymltest
summary.prop.part	boot.phylo
theta.h	ape-defunct
theta.k	ape-defunct
theta.s	ape-defunct
tiplabels	nodelabels
tree.build	ape-internal
unique.multiPhylo	unique.multiPhylo
unroot	root
unrooted.plot	ape-internal
unrooted.xy	ape-internal
varcomp	varcomp
vcv	vcv.phylo
vcv.corPhyl	vcv.phylo
vcv.phylo	vcv.phylo
weight.taxo	weight.taxo
weight.taxo2	weight.taxo
which.edge	which.edge
woodmouse	woodmouse
write.dna	write.dna
write.nexus	write.nexus
write.nexus.data	write.nexus.data
write.tree	write.tree
yule	yule
yule.cov	yule.cov
yule.time	yule.time
zoom	zoom
[.DNAbin	DNAbin
[.multiPhylo	print.phylo
[[.multiPhylo	print.phylo
