phytools-package	phytools-package
add.arrow	add.arrow
add.color.bar	add.color.bar
add.everywhere	add.everywhere
add.random	add.random
add.simmap.legend	add.simmap.legend
add.species.to.genus	add.species.to.genus
aic.w	aic.w
allFurcTrees	allFurcTrees
allRotations	rotateNodes
anc.Bayes	anc.Bayes
anc.ML	anc.ML
anc.trend	anc.trend
ancThresh	ancThresh
anole.data	anoletree
anoletree	anoletree
applyBranchLengths	applyBranchLengths
arc.cladelabels	cladelabels
as.multiPhylo	as.multiPhylo
as.multiPhylo.multiSimmap	as.multiPhylo
as.multiPhylo.phylo	as.multiPhylo
as.Qmatrix	as.Qmatrix
as.Qmatrix.fitMk	as.Qmatrix
ave.rates	ave.rates
averageTree	averageTree
backbone.toPhylo	phylo.toBackbone
bd	bd
bind.tip	bind.tip
bind.tree.simmap	bind.tree.simmap
biplot.phyl.pca	phyl.pca
bmPlot	bmPlot
branching.diffusion	branching.diffusion
brownie.lite	brownie.lite
brownieREML	brownieREML
cladelabels	cladelabels
coef.phyl.RMA	phyl.RMA
collapse.to.star	collapse.to.star
collapseTree	collapseTree
compare.chronograms	compare.chronograms
compute.mr	mrp.supertree
consensus.edges	consensus.edges
contMap	contMap
cophylo	cophylo
cospeciation	cospeciation
countSimmap	countSimmap
ctt	ctt
density.anc.Bayes	anc.Bayes
density.mcmcMk	fitMk
density.multiSimmap	density.multiSimmap
densityMap	densityMap
densityTree	densityTree
describe.simmap	describe.simmap
di2multi.contMap	di2multi.simmap
di2multi.densityMap	di2multi.simmap
di2multi.multiSimmap	di2multi.simmap
di2multi.simmap	di2multi.simmap
dot.legend	dotTree
dotTree	dotTree
drop.clade	drop.clade
drop.leaves	drop.leaves
drop.tip.contMap	drop.tip.contMap
drop.tip.densityMap	drop.tip.contMap
drop.tip.simmap	drop.tip.simmap
drop.tip.singleton	map.to.singleton
Dtest	Dtest
edgelabels.cophylo	nodelabels.cophylo
edgeProbs	edgeProbs
errorbar.contMap	contMap
estDiversity	estDiversity
evol.rate.mcmc	evol.rate.mcmc
evol.vcv	evol.vcv
evolvcv.lite	evolvcv.lite
exhaustiveMP	exhaustiveMP
expand.clade	expand.clade
export.as.xml	export.as.xml
extract.clade.simmap	drop.tip.simmap
extract.strahlerNumber	strahlerNumber
fancyTree	fancyTree
fastAnc	fastAnc
fastBM	fastBM
fastDist	fastMRCA
fastHeight	fastMRCA
fastMRCA	fastMRCA
findMRCA	findMRCA
fit.bd	fit.bd
fit.yule	fit.bd
fitBayes	fitBayes
fitDiversityModel	fitDiversityModel
fitMk	fitMk
fitmultiMk	fitMk
fitPagel	fitPagel
fitpolyMk	fitMk
force.ultrametric	force.ultrametric
gammatest	gammatest
genSeq	genSeq
genus.to.species.tree	add.species.to.genus
geo.legend	geo.legend
geo.palette	geo.legend
get.treepos	get.treepos
getCladesofSize	getCladesofSize
getDescendants	getDescendants
getExtant	getExtant
getExtinct	getExtant
getnode	get.treepos
getParent	getDescendants
getSisters	getSisters
getStates	getStates
gtt	ltt
labelnodes	labelnodes
ladderize.simmap	ladderize.simmap
lambda.transform	lambda.transform
lik.bd	fit.bd
likMlambda	likMlambda
likSurface.rateshift	rateshift
linklabels	linklabels
locate.fossil	locate.fossil
locate.yeti	locate.yeti
logLik.fitDiversityModel	fitDiversityModel
ls.consensus	averageTree
ls.tree	ls.tree
ltt	ltt
ltt95	ltt95
make.era.map	make.era.map
make.simmap	make.simmap
make.transparent	densityTree
mammal.data	anoletree
mammal.tree	anoletree
Map.Overlap	map.overlap
map.overlap	map.overlap
map.to.singleton	map.to.singleton
mapped.states	mapped.states
markChanges	markChanges
matchLabels	matchNodes
matchNodes	matchNodes
mccr	ltt
mcmcMk	fitMk
mergeMappedStates	mergeMappedStates
midpoint.root	midpoint.root
minRotate	minRotate
minSplit	minSplit
minTreeDist	averageTree
modified.Grafen	modified.Grafen
mrp.supertree	mrp.supertree
multi.mantel	multi.mantel
multi2di.contMap	di2multi.simmap
multi2di.densityMap	di2multi.simmap
multi2di.multiSimmap	di2multi.simmap
multi2di.simmap	di2multi.simmap
multiC	multiC
multiOU	sim.rates
multiRF	multiRF
node.paths	modified.Grafen
nodeheight	nodeHeights
nodeHeights	nodeHeights
nodelabels.cophylo	nodelabels.cophylo
optim.phylo.ls	optim.phylo.ls
orderMappedEdge	orderMappedEdge
paintBranches	paintSubTree
paintSubTree	paintSubTree
paste.tree	paste.tree
pbtree	pbtree
pgls.Ives	pgls.Ives
pgls.SEy	pgls.Ives
phenogram	phenogram
phenogram95	fancyTree
phyl.cca	phyl.cca
phyl.pairedttest	phyl.pairedttest
phyl.pca	phyl.pca
phyl.resid	phyl.resid
phyl.RMA	phyl.RMA
phyl.vcv	phyl.vcv
phylANOVA	phylANOVA
phylo.heatmap	phylo.heatmap
phylo.impute	phylo.impute
phylo.to.map	phylo.to.map
phylo.toBackbone	phylo.toBackbone
phyloDesign	phyloDesign
phylomorphospace	phylomorphospace
phylomorphospace3d	phylomorphospace3d
phyloScattergram	fancyTree
phylosig	phylosig
phytools	phytools-package
plot.anc.Bayes	anc.Bayes
plot.backbonePhylo	plot.backbonePhylo
plot.changesMap	density.multiSimmap
plot.contMap	contMap
plot.cophylo	cophylo
plot.cospeciation	cospeciation
plot.density.mcmcMk	fitMk
plot.densityMap	densityMap
plot.describe.simmap	describe.simmap
plot.expand.clade	expand.clade
plot.fitMk	fitMk
plot.fitPagel	fitPagel
plot.fitpolyMk	fitMk
plot.gfit	fitMk
plot.ltt95	ltt95
plot.mcmcMk	fitMk
plot.multiSimmap	plotSimmap
plot.phyl.RMA	phyl.RMA
plot.phylo.to.map	phylo.to.map
plot.phylosig	phylosig
plot.Qmatrix	as.Qmatrix
plot.rateshift	rateshift
plot.simBMphylo	simBMphylo
plot.simmap	plotSimmap
plot.summary.evol.rate.mcmc	evol.rate.mcmc
plotBranchbyTrait	plotBranchbyTrait
plotSimmap	plotSimmap
plotThresh	plotThresh
plotTree	plotTree
plotTree.barplot	plotTree.wBars
plotTree.boxplot	plotTree.wBars
plotTree.datamatrix	plotTree.datamatrix
plotTree.errorbars	plotTree.errorbars
plotTree.singletons	map.to.singleton
plotTree.splits	splitplotTree
plotTree.wBars	plotTree.wBars
posterior.evolrate	posterior.evolrate
posthoc	posthoc
posthoc.ratebytree	ratebytree
print.backbonePhylo	print.backbonePhylo
print.cospeciation	cospeciation
print.evol.rate.mcmc	evol.rate.mcmc
print.fit.bd	fit.bd
print.fitDiversityModel	fitDiversityModel
print.Qmatrix	as.Qmatrix
print.summary.evol.rate.mcmc	evol.rate.mcmc
project.phylomorphospace	phylomorphospace
ratebystate	ratebystate
ratebytree	ratebytree
rateshift	rateshift
read.newick	read.newick
read.simmap	read.simmap
reorder.backbonePhylo	reorder.backbonePhylo
reorderSimmap	reorderSimmap
rep.multiPhylo	rep.phylo
rep.phylo	rep.phylo
repPhylo	rep.phylo
reroot	reroot
rerootingMethod	rerootingMethod
rescaleSimmap	rescaleSimmap
resolveAllNodes	resolveNode
resolveNode	resolveNode
rootedge.to.singleton	map.to.singleton
rotate.multi	rotateNodes
rotateNodes	rotateNodes
roundBranches	roundBranches
roundPhylogram	roundPhylogram
rstate	rstate
salamanders	anoletree
sampleFrom	sampleFrom
scores	phyl.pca
scores.phyl.pca	phyl.pca
setMap	setMap
setMap.contMap	setMap
setMap.densityMap	setMap
setMap.phyloScattergram	setMap
sim.corrs	sim.corrs
sim.ctt	ctt
sim.history	sim.history
sim.Mk	sim.history
sim.multiCtt	ctt
sim.multiMk	sim.history
sim.ratebystate	sim.ratebystate
sim.rates	sim.rates
simBMphylo	simBMphylo
skewers	skewers
splitEdgeColor	splitEdgeColor
splitplotTree	splitplotTree
splitTree	splitTree
starTree	starTree
strahlerNumber	strahlerNumber
summary.evol.rate.mcmc	evol.rate.mcmc
summary.multiSimmap	describe.simmap
summary.simmap	describe.simmap
sunfish.data	anoletree
sunfish.tree	anoletree
threshBayes	threshBayes
threshDIC	threshDIC
threshState	threshState
tiplabels.cophylo	nodelabels.cophylo
tipRotate	minRotate
to.matrix	to.matrix
tree.grow	tree.grow
treeSlice	treeSlice
untangle	untangle
vcvPhylo	vcvPhylo
wasp.data	anoletree
wasp.trees	anoletree
write.simmap	write.simmap
writeAncestors	writeAncestors
writeNexus	writeNexus
