ape-package	ape-package
$.multiPhylo	multiphylo
$<-.multiPhylo	multiphylo
+.phylo	bind.tree
.compressTipLabel	c.phylo
.PlotPhyloEnv	ape-internal
.uncompressTipLabel	c.phylo
AAbin	AAbin
AAsubst	AAbin
abbreviateGenus	label2table
ace	ace
add.scale.bar	add.scale.bar
additive	additive
AIC.ace	ace
alex	alex
all.equal.DNAbin	all.equal.DNAbin
all.equal.phylo	all.equal.phylo
alview	alview
anova.ace	ace
ape	ape-package
apetools	apetools
arecompatible	is.compatible
as.AAbin	AAbin
as.AAbin.AAMultipleAlignment	AAbin
as.AAbin.AAString	AAbin
as.AAbin.AAStringSet	AAbin
as.AAbin.character	AAbin
as.AAbin.list	AAbin
as.alignment	as.alignment
as.bitsplits	as.bitsplits
as.bitsplits.prop.part	as.bitsplits
as.character.AAbin	AAbin
as.character.DNAbin	as.alignment
as.DNAbin	as.alignment
as.DNAbin.alignment	as.alignment
as.DNAbin.character	as.alignment
as.DNAbin.DNAMultipleAlignment	as.alignment
as.DNAbin.DNAString	as.alignment
as.DNAbin.DNAStringSet	as.alignment
as.DNAbin.list	as.alignment
as.DNAbin.PairwiseAlignmentsSingleSubject	as.alignment
as.evonet	evonet
as.evonet.phylo	evonet
as.hclust.phylo	as.phylo
as.igraph	as.phylo
as.igraph.evonet	evonet
as.igraph.phylo	as.phylo
as.list.AAbin	AAbin
as.list.DNAbin	DNAbin
as.matching	as.matching
as.matching.phylo	as.matching
as.matrix.AAbin	AAbin
as.matrix.DNAbin	DNAbin
as.network.evonet	evonet
as.network.phylo	as.phylo
as.networx.evonet	evonet
as.phyDat.AAbin	AAbin
as.phylo	as.phylo
as.phylo.default	as.phylo
as.phylo.evonet	evonet
as.phylo.formula	as.phylo.formula
as.phylo.hclust	as.phylo
as.phylo.matching	as.matching
as.phylo.phylog	as.phylo
as.prop.part	as.bitsplits
as.prop.part.bitsplits	as.bitsplits
axisPhylo	axisPhylo
balance	balance
base.freq	base.freq
bd.ext	bd.ext
bd.time	bd.time
binaryPGLMM	binaryPGLMM
binaryPGLMM.sim	binaryPGLMM
bind.tree	bind.tree
bionj	bionj
bionjs	njs
biplot.pcoa	pcoa
bird.families	bird.families
bird.orders	bird.orders
birthdeath	birthdeath
bitsplits	as.bitsplits
boot.phylo	boot.phylo
BOTHlabels	ape-internal
branching.times	branching.times
bydir	apetools
c.AAbin	AAbin
c.DNAbin	DNAbin
c.multiPhylo	c.phylo
c.phylo	c.phylo
CADM	CADM.global
CADM.global	CADM.global
CADM.post	CADM.global
carnivora	carnivora
cbind.AAbin	AAbin
cbind.DNAbin	DNAbin
checkAlignment	checkAlignment
checkLabel	checkLabel
checkValidPhylo	checkValidPhylo
cherry	cherry
chiroptera	chiroptera
chronoMPL	chronoMPL
chronopl	chronopl
chronos	chronos
chronos.control	chronos
circular.plot	ape-internal
cladewise	reorder.phylo
cladogram.plot	ape-internal
clustal	clustal
clustalomega	clustal
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
comparePhylo	comparePhylo
complement	trans
compute.brlen	compute.brlen
compute.brtime	compute.brtime
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
corphylo	corphylo
correlogram.formula	correlogram.formula
countBipartitions	as.bitsplits
cynipids	cynipids
data.nex	cynipids
dbd	dbd
dbdTime	dbd
def	def
degree	degree
degree.evonet	degree
degree.phylo	degree
del.colgapsonly	del.gaps
del.gaps	del.gaps
del.rowgapsonly	del.gaps
delta.plot	delta.plot
deviance.ace	ace
di2multi	multi2di
di2multi.multiPhylo	multi2di
di2multi.phylo	multi2di
dist.aa	AAbin
dist.dna	dist.dna
dist.gene	dist.gene
dist.nodes	cophenetic.phylo
dist.topo	dist.topo
diversi.gof	diversi.gof
diversi.time	diversi.time
diversity.contrast.test	diversity.contrast.test
DNAbin	DNAbin
DNAbin2indel	DNAbin2indel
dnds	dnds
drawSupportOnEdges	plot.phyloExtra
drop.fossil	rlineage
drop.tip	drop.tip
drop.tip.multiPhylo	drop.tip
drop.tip.phylo	drop.tip
drop1.compar.gee	compar.gee
dyule	dbd
edgelabels	nodelabels
edges	edges
editFileExtensions	apetools
efastats	clustal
estimate.dates	node.dating
estimate.mu	node.dating
evonet	evonet
ewLasso	ewLasso
extract.clade	drop.tip
extract.popsize	mcmc.popsize
fancyarrows	edges
FastME	fastme
fastme	fastme
fastme.bal	fastme
fastme.ols	fastme
find.skyline.epsilon	skyline
floating.pie.asp	ape-internal
Ftab	base.freq
gammaStat	gammaStat
GC.content	base.freq
getAnnotationsGenBank	getAnnotationsGenBank
getMRCA	mrca
gopher.D	parafit
has.singles	collapse.singles
hivtree	hivtree
hivtree.newick	hivtree
hivtree.table	hivtree
howmanytrees	howmanytrees
HP.links	parafit
identify.phylo	identify.phylo
image.AAbin	AAbin
image.DNAbin	image.DNAbin
Initialize.corPhyl	Initialize.corPhyl
is.binary	is.binary.tree
is.binary.multiPhylo	is.binary.tree
is.binary.phylo	is.binary.tree
is.binary.tree	is.binary.tree
is.compatible	is.compatible
is.compatible.bitsplits	is.compatible
is.monophyletic	is.monophyletic
is.rooted	root
is.rooted.multiPhylo	root
is.rooted.phylo	root
is.ultrametric	is.ultrametric
is.ultrametric.multiPhylo	is.ultrametric
is.ultrametric.phylo	is.ultrametric
keep.tip	drop.tip
keep.tip.multiPhylo	drop.tip
keep.tip.phylo	drop.tip
kronoviz	kronoviz
label2table	label2table
labels.AAbin	AAbin
labels.DNAbin	DNAbin
ladderize	ladderize
LargeNumber	howmanytrees
latag2n	latag2n
letterconf	clustal
lice.D	parafit
lines.popsize	mcmc.popsize
lines.skyline	skylineplot
lmorigin	lmorigin
lmorigin.ex1	lmorigin
lmorigin.ex2	lmorigin
logLik.ace	ace
LTT	LTT
ltt.coplot	ltt.plot
ltt.lines	ltt.plot
ltt.plot	ltt.plot
ltt.plot.coords	ltt.plot
makeChronosCalib	chronos
makeLabel	makeLabel
makeLabel.character	makeLabel
makeLabel.DNAbin	makeLabel
makeLabel.multiPhylo	makeLabel
makeLabel.phylo	makeLabel
makeNodeLabel	makeNodeLabel
makeNodeLabel.multiPhylo	makeNodeLabel
makeNodeLabel.phylo	makeNodeLabel
mantel.test	mantel.test
mat3	mat3
mat5M3ID	mat5M3ID
mat5Mrand	mat5Mrand
matching	as.matching
matexpo	matexpo
mcconwaysims.test	mcconwaysims.test
mcmc.popsize	mcmc.popsize
mixedFontLabel	mixedFontLabel
mltt.plot	ltt.plot
Moran.I	MoranI
MPR	MPR
mrca	mrca
mst	mst
multi2di	multi2di
multi2di.multiPhylo	multi2di
multi2di.phylo	multi2di
multiphylo	multiphylo
muscle	clustal
muscle5	clustal
mvr	mvr
mvrs	mvr
Nedge	summary.phylo
Nedge.evonet	evonet
Nedge.multiPhylo	summary.phylo
Nedge.phylo	summary.phylo
new2old.phylo	as.phylo
nexus2DNAbin	read.nexus.data
nj	nj
njs	njs
Nnode	summary.phylo
Nnode.multiPhylo	summary.phylo
Nnode.phylo	summary.phylo
node.dating	node.dating
node.depth	node.depth
node.depth.edgelength	node.depth
node.height	node.depth
nodelabels	nodelabels
nodepath	nodepath
node_depth	ape-internal
node_depth_edgelength	ape-internal
node_height	ape-internal
node_height_clado	ape-internal
Ntip	summary.phylo
Ntip.multiPhylo	summary.phylo
Ntip.phylo	summary.phylo
old2new.phylo	as.phylo
ONEwise	ape-internal
parafit	parafit
pcoa	pcoa
perm.rowscols	ape-internal
phydataplot	phydataplot
phylo	read.tree
phylogram.plot	ape-internal
phymltest	phymltest
pic	pic
pic.ortho	pic.ortho
plot.correlogram	plot.correlogram
plot.correlogramList	plot.correlogram
plot.evonet	evonet
plot.mst	mst
plot.multiPhylo	plot.phylo
plot.phylo	plot.phylo
plot.phylo.extra	plot.phyloExtra
plot.phymltest	phymltest
plot.popsize	mcmc.popsize
plot.prop.part	boot.phylo
plot.skyline	skylineplot
plot.varcomp	plot.varcomp
plotBreakLongEdges	plot.phyloExtra
plotPhyloCoor	ape-internal
plotTreeTime	plotTreeTime
polar2rect	ape-internal
postorder	reorder.phylo
postprocess.prop.part	ape-internal
predict.compar.gee	compar.gee
print.AAbin	AAbin
print.ace	ace
print.binaryPGLMM	binaryPGLMM
print.birthdeath	birthdeath
print.bitsplits	as.bitsplits
print.chronos	chronos
print.compar.gee	compar.gee
print.comparePhylo	comparePhylo
print.corphylo	corphylo
print.DNAbin	DNAbin
print.evonet	evonet
print.LargeNumber	howmanytrees
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
rbdtree	rlineage
rbind.AAbin	AAbin
rbind.DNAbin	DNAbin
rcoal	rtree
rDNAbin	rDNAbin
read.caic	read.caic
read.dna	read.dna
read.evonet	evonet
read.FASTA	read.dna
read.fastq	read.dna
read.GenBank	read.GenBank
read.gff	read.gff
read.nexus	read.nexus
read.nexus.data	read.nexus.data
read.tree	read.tree
reconstruct	reconstruct
rect2polar	ape-internal
reorder.evonet	evonet
reorder.multiPhylo	reorder.phylo
reorder.phylo	reorder.phylo
reorderRcpp	ape-internal
richness.yule.test	richness.yule.test
ring	phydataplot
rlineage	rlineage
rmtopology	rtree
rmtree	rtree
root	root
root.multiPhylo	root
root.phylo	root
rotate	rotate
rotateConstr	rotate
rphylo	rlineage
rtopology	rtree
rTraitCont	rTraitCont
rTraitDisc	rTraitDisc
rTraitMult	rTraitMult
rtree	rtree
rtt	rtt
SDM	SDM
seg.sites	seg.sites
seq_root2tip	ape-internal
SHORTwise	ape-internal
skyline	skyline
skyline.coalescentIntervals	skyline
skyline.collapsedIntervals	skyline
skyline.phylo	skyline
skylineplot	skylineplot
skylineplot.deluxe	skylineplot
slowinskiguyer.test	slowinskiguyer.test
solveAmbiguousBases	solveAmbiguousBases
sort.bitsplits	as.bitsplits
speciesTree	speciesTree
str.multiPhylo	print.phylo
stree	stree
stripLabel	label2table
subtreeplot	subtreeplot
subtrees	subtrees
summary.phylo	summary.phylo
summary.phymltest	phymltest
summary.prop.part	boot.phylo
tcoffee	clustal
tiplabels	nodelabels
trans	trans
treePop	treePop
trex	trex
triangMtd	triangMtd
triangMtds	triangMtd
ultrametric	additive
unique.multiPhylo	unique.multiPhylo
unroot	root
unroot.multiPhylo	root
unroot.phylo	root
unrooted.xy	ape-internal
updateLabel	updateLabel
updateLabel.AAbin	updateLabel
updateLabel.character	updateLabel
updateLabel.data.frame	updateLabel
updateLabel.DNAbin	updateLabel
updateLabel.evonet	updateLabel
updateLabel.matrix	updateLabel
updateLabel.phylo	updateLabel
varcomp	varcomp
varCompPhylip	varCompPhylip
vcv	vcv.phylo
vcv.corPhyl	vcv.phylo
vcv.phylo	vcv.phylo
vcv2phylo	vcv2phylo
weight.taxo	weight.taxo
weight.taxo2	weight.taxo
where	where
which.edge	which.edge
woodmouse	woodmouse
write.dna	write.dna
write.evonet	evonet
write.FASTA	write.dna
write.nexus	write.nexus
write.nexus.data	write.nexus.data
write.tree	write.tree
Xplor	apetools
Xplorefiles	apetools
yule	yule
yule.cov	yule.cov
yule.time	yule.time
zoom	zoom
[.AAbin	AAbin
[.DNAbin	DNAbin
[.multiPhylo	multiphylo
[<-.multiPhylo	multiphylo
[[.multiPhylo	multiphylo
[[<-.multiPhylo	multiphylo
