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
ancr	ancr
ancThresh	ancThresh
anole.data	anoletree
anoletree	anoletree
ansi_phylo	ansi_phylo
ant.geog	anoletree
ant.tree	anoletree
applyBranchLengths	applyBranchLengths
arc.cladelabels	cladelabels
as.multiPhylo	as.multiPhylo
as.multiPhylo.multiSimmap	as.multiPhylo
as.multiPhylo.phylo	as.multiPhylo
as.prcomp	phyl.pca
as.princomp	phyl.pca
as.Qmatrix	as.Qmatrix
as.Qmatrix.fitMk	as.Qmatrix
ave.rates	ave.rates
averageTree	averageTree
backbone.toPhylo	phylo.toBackbone
bat.tree	anoletree
bat_virus.data	anoletree
bd	bd
betaCoV.tree	anoletree
bind.tip	bind.tip
bind.tree.simmap	bind.tree.simmap
biplot.phyl.pca	phyl.pca
bmPlot	bmPlot
bonyfish.data	anoletree
bonyfish.tree	anoletree
bounded_bm	bounded_bm
branching.diffusion	branching.diffusion
brownie.lite	brownie.lite
brownieREML	brownieREML
butterfly.data	anoletree
butterfly.tree	anoletree
cladebox	cladelabels
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
cordylid.data	anoletree
cordylid.tree	anoletree
cospeciation	cospeciation
cotangleplot	cophylo
countSimmap	countSimmap
ctt	ctt
darter.tree	anoletree
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.multiSimmap	drop.tip.multiSimmap
drop.tip.simmap	drop.tip.simmap
drop.tip.singleton	map.to.singleton
Dtest	Dtest
edge.widthMap	edge.widthMap
edgelabels.cophylo	nodelabels.cophylo
edgeProbs	edgeProbs
eel.data	anoletree
eel.tree	anoletree
elapidae.tree	anoletree
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
fitcontMk	fitcontMk
fitDiversityModel	fitDiversityModel
fitfnMk	fitMk
fitgammaMk	fitMk
fitHRM	fitMk
fitMk	fitMk
fitMk.parallel	fitMk
fitmultiBM	fitmultiBM
fitmultiMk	fitMk
fitmultiTrend	fitmultiBM
fitPagel	fitPagel
fitpolyMk	fitMk
fitsemiThresh	fitThresh
fitThresh	fitThresh
flatworm.data	anoletree
flatworm.tree	anoletree
force.ultrametric	force.ultrametric
gammatest	gammatest
gamma_pruning	gamma_pruning
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
graph.polyMk	fitMk
gtt	ltt
hide.hidden	ancr
keep.tip.contMap	drop.tip.contMap
keep.tip.densityMap	drop.tip.contMap
keep.tip.multiSimmap	drop.tip.multiSimmap
keep.tip.simmap	drop.tip.simmap
labelnodes	labelnodes
ladderize.simmap	ladderize.simmap
lambda.transform	lambda.transform
lik.bd	fit.bd
likMlambda	likMlambda
likSurface.rateshift	rateshift
linklabels	linklabels
liolaemid.data	anoletree
liolaemid.tree	anoletree
locate.fossil	locate.fossil
locate.yeti	locate.yeti
logLik.fitDiversityModel	fitDiversityModel
ls.consensus	averageTree
ls.tree	ls.tree
ltt	ltt
ltt.multiPhylo	ltt
ltt.multiSimmap	ltt
ltt.phylo	ltt
ltt.simmap	ltt
ltt95	ltt95
make.era.map	make.era.map
make.simmap	make.simmap
make.transparent	densityTree
mammal.data	anoletree
mammal.geog	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
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
multirateBM	multirateBM
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.ancr	ancr
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.edge.widthMap	edge.widthMap
plot.expand.clade	expand.clade
plot.fitHRM	fitMk
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
plotFanTree.wTraits	plotTree.datamatrix
plotSimmap	plotSimmap
plotThresh	plotThresh
plotTree	plotTree
plotTree.barplot	plotTree.wBars
plotTree.boxplot	plotTree.wBars
plotTree.datamatrix	plotTree.datamatrix
plotTree.errorbars	plotTree.errorbars
plotTree.lollipop	plotTree.lollipop
plotTree.singletons	map.to.singleton
plotTree.splits	splitplotTree
plotTree.wBars	plotTree.wBars
posterior.evolrate	posterior.evolrate
posthoc	posthoc
posthoc.ratebytree	ratebytree
primate.data	anoletree
primate.tree	anoletree
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
pscore	pscore
ratebystate	ratebystate
ratebytree	ratebytree
rateshift	rateshift
read.newick	read.newick
read.simmap	read.simmap
readNexus	read.newick
reorder.backbonePhylo	reorder.backbonePhylo
reorderSimmap	reorderSimmap
rep.multiPhylo	rep.phylo
rep.phylo	rep.phylo
repPhylo	rep.phylo
reroot	reroot
rerootingMethod	rerootingMethod
rescale	rescale
rescale.multiSimmap	rescaleSimmap
rescale.simmap	rescaleSimmap
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.multirateBM_plot	setMap
setMap.phyloScattergram	setMap
sigmoidPhylogram	roundPhylogram
sim.absorbing	bmPlot
sim.corrs	sim.corrs
sim.ctt	ctt
sim.history	sim.history
sim.Mk	sim.history
sim.multiCtt	ctt
sim.multiMk	sim.history
sim.multiTrend	bmPlot
sim.ratebystate	sim.ratebystate
sim.rates	sim.rates
sim.reflective	bmPlot
simBMphylo	simBMphylo
simmap	make.simmap
skewers	skewers
splinePhylogram	roundPhylogram
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
tortoise.geog	anoletree
tortoise.tree	anoletree
tree.grow	tree.grow
treeSlice	treeSlice
tropidurid.data	anoletree
tropidurid.tree	anoletree
untangle	untangle
vcvPhylo	vcvPhylo
vertebrate.data	anoletree
vertebrate.tree	anoletree
wasp.data	anoletree
wasp.trees	anoletree
whale.tree	anoletree
write.simmap	write.simmap
writeAncestors	writeAncestors
writeNexus	writeNexus
