add.scale.bar	add.scale.bar
all.equal.phylo	all.equal.phylo
as.hclust.phylo	as.phylo
as.matching	as.matching
as.matching.phylo	as.matching
as.phylo	as.phylo
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
bird.families	bird.families
bird.orders	bird.orders
birth.step	ape-internal
birthdeath	birthdeath
boot.phylo	boot.phylo
branching.times	branching.times
buildTreeFromPhylo	ape-internal
carnivora	carnivora
cherry	cherry
chiroptera	chiroptera
chronogram	chronogram
clado.build	ape-internal
cladogram.plot	ape-internal
coalescent.intervals	coalescent.intervals
coalescent.intervals.default	coalescent.intervals
coalescent.intervals.phylo	coalescent.intervals
coef.corBrownian	corBrownian
coef.corGrafen	corGrafen
coef.corMartins	corMartins
collapsed.intervals	collapsed.intervals
compar.cheverud	compar.cheverud
compar.gee	compar.gee
compar.lynch	compar.lynch
compute.brlen	compute.brlen
corBrownian	corBrownian
corClasses	corClasses
corGrafen	corGrafen
corMartins	corMartins
corMatrix.corBrownian	corBrownian
corMatrix.corGrafen	corGrafen
corMatrix.corMartins	corMartins
corPhyl	corClasses
Correlogram	Correlogram
correlogram.formula	Correlogram
correlogram.phylo	Correlogram
death.step	ape-internal
destroyTree	ape-internal
di2multi	multi2di
discrete.dist	discrete.dist
dist.dna	dist.dna
dist.gene	dist.gene
dist.gene.pairwise	dist.gene
dist.gene.percentage	dist.gene
dist.phylo	dist.phylo
dist.taxo	dist.taxo
dist.topo	dist.topo
diversi.gof	diversi.gof
diversi.time	diversi.time
drop.tip	drop.tip
extract.popsize	mcmc.popsize
f.cherry.uniform	ape-internal
f.cherry.yule	ape-internal
find.skyline.epsilon	skyline
gammaStat	gammaStat
GC.content	GC.content
getDurations	ape-internal
getEdgeLengths	ape-internal
getError	ape-internal
getExternalParams	ape-internal
getMisawaTajima	ape-internal
getNEdges	ape-internal
getNFreeParams	ape-internal
getRates	ape-internal
H	heterozygosity
heterozygosity	heterozygosity
hivtree	hivtree
hivtree.newick	hivtree
hivtree.table	hivtree
howmanytrees	howmanytrees
ht.move	ape-internal
Initialize.corPhyl	Initialize.corPhyl
is.binary.tree	is.binary.tree
is.ultrametric	is.ultrametric
klastorin	klastorin
landplants	landplants
landplants.newick	landplants
lines.popsize	mcmc.popsize
lines.skyline	skylineplot
loglik.pop	ape-internal
lower.triang	ape-internal
ltt.lines	ltt.plot
ltt.plot	ltt.plot
mant.zstat	ape-internal
mantel.test	mantel.test
mcmc.popsize	mcmc.popsize
mltt.plot	ltt.plot
Moran.I	MoranI
mst	mst
multi2di	multi2di
nEdges	ape-internal
nj	nj
nNodes	ape-internal
node.depth	node.depth
node.height	ape-internal
node.height.clado	ape-internal
node.leafnumber	node.leafnumber
node.sons	node.sons
nodelabels	nodelabels
NPRS.criterion	NPRS.criterion
nsca	ape-internal
nTips	ape-internal
nuc.div	nuc.div
objFuncLogScale	ape-internal
opsin	opsin
opsin.newick	opsin
optimTree	ape-internal
panel.superpose.correlogram	panel.superpose.correlogram
perm.rowscols	ape-internal
phylogram	ape-internal
phylogram.plot	ape-internal
phymltest	phymltest
pic	pic
plot.correlogram	plot.correlogram
plot.correlogramList	plot.correlogramList
plot.mst	mst
plot.phylo	plot.phylo
plot.phymltest	phymltest
plot.popsize	mcmc.popsize
plot.skyline	skylineplot
plot.varcomp	plot.varcomp
pos.move	ape-internal
prepareTree	ape-internal
print.birthdeath	birthdeath
print.compar.gee	compar.gee
print.phymltest	phymltest
prop.clades	boot.phylo
prop.part	boot.phylo
ratogram	ratogram
read.dna	read.dna
read.GenBank	read.GenBank
read.nexus	read.nexus
read.tree	read.tree
root	root
rotate	rotate
rtree	rtree
seg.sites	seg.sites
setTree	ape-internal
skyline	skyline
skyline.coalescentIntervals	skyline
skyline.collapsedIntervals	skyline
skyline.phylo	skyline
skylineplot	skylineplot
skylineplot.deluxe	skylineplot
sort.index	ape-internal
summary.phylo	summary.phylo
summary.phymltest	phymltest
theta.h	theta.h
theta.k	theta.k
theta.s	theta.s
tree.build	ape-internal
unrooted.plot	ape-internal
unrooted.xy	ape-internal
varcomp	varcomp
vcv.phylo	vcv.phylo
which.edge	which.edge
woodmouse	woodmouse
write.dna	write.dna
write.nexus	write.nexus
write.tree	write.tree
xenarthra	xenarthra
yule	yule
yule.cov	yule.cov
zoom	zoom
