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
allFurcTrees	allFurcTrees
anc.Bayes	anc.Bayes
anc.ML	anc.ML
anc.trend	anc.trend
ancThresh	ancThresh
anoletree	anoletree
applyBranchLengths	applyBranchLengths
ave.rates	ave.rates
backbone.toPhylo	phylo.toBackbone
bind.tip	bind.tip
biplot.phyl.pca	phyl.pca
bmPlot	bmPlot
branching.diffusion	branching.diffusion
brownie.lite	brownie.lite
brownieREML	brownieREML
cladelabels	cladelabels
collapse.to.star	collapse.to.star
collapseTree	collapseTree
contMap	contMap
countSimmap	countSimmap
densityMap	densityMap
describe.simmap	describe.simmap
di2multi.simmap	di2multi.simmap
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
estDiversity	estDiversity
evol.rate.mcmc	evol.rate.mcmc
evol.vcv	evol.vcv
evolvcv.lite	evolvcv.lite
exhaustiveMP	exhaustiveMP
expm	expm
export.as.xml	export.as.xml
extract.clade.simmap	drop.tip.simmap
extract.strahlerNumber	strahlerNumber
fancyTree	fancyTree
fastAnc	fastAnc
fastBM	fastBM
fastHeight	fastMRCA
fastMRCA	fastMRCA
findMRCA	findMRCA
fitBayes	fitBayes
fitDiversityModel	fitDiversityModel
fitPagel	fitPagel
gammatest	gammatest
genSeq	genSeq
getCladesofSize	getCladesofSize
getDescendants	getDescendants
getExtant	getExtant
getExtinct	getExtant
getSisters	getSisters
getStates	getStates
ladderize.simmap	ladderize.simmap
lambda.transform	lambda.transform
likMlambda	likMlambda
locate.fossil	locate.fossil
locate.yeti	locate.yeti
ls.tree	ls.tree
ltt	ltt
ltt95	ltt95
make.era.map	make.era.map
make.simmap	make.simmap
map.overlap	map.overlap
map.to.singleton	map.to.singleton
matchNodes	matchNodes
mergeMappedStates	mergeMappedStates
midpoint.root	midpoint.root
minRotate	minRotate
minSplit	minSplit
mrp.supertree	mrp.supertree
multi.mantel	multi.mantel
multiC	multiC
multiRF	multiRF
nodeheight	nodeHeights
nodeHeights	nodeHeights
optim.phylo.ls	optim.phylo.ls
orderMappedEdge	orderMappedEdge
paintBranches	paintSubTree
paintSubTree	paintSubTree
paste.tree	paste.tree
pbtree	pbtree
pgls.Ives	pgls.Ives
phenogram	phenogram
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.to.map	phylo.to.map
phylo.toBackbone	phylo.toBackbone
phyloDesign	phyloDesign
phylomorphospace	phylomorphospace
phylomorphospace3d	phylomorphospace3d
phylosig	phylosig
phytools	phytools-package
plot.backbonePhylo	plot.backbonePhylo
plot.contMap	contMap
plot.densityMap	densityMap
plot.ltt95	ltt95
plot.phylo.to.map	phylo.to.map
plotBranchbyTrait	plotBranchbyTrait
plotSimmap	plotSimmap
plotThresh	plotThresh
plotTree	plotTree
plotTree.singletons	map.to.singleton
plotTree.wBars	plotTree.wBars
posterior.evolrate	posterior.evolrate
print.backbonePhylo	print.backbonePhylo
ratebystate	ratebystate
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
rotateNodes	rotateNodes
roundBranches	roundBranches
roundPhylogram	roundPhylogram
rstate	rstate
sampleFrom	sampleFrom
setMap	setMap
sim.corrs	sim.corrs
sim.history	sim.history
sim.ratebystate	sim.ratebystate
sim.rates	sim.rates
skewers	skewers
splitplotTree	splitplotTree
splitTree	splitTree
starTree	starTree
strahlerNumber	strahlerNumber
threshBayes	threshBayes
threshDIC	threshDIC
threshState	threshState
to.matrix	to.matrix
treeSlice	treeSlice
untangle	untangle
vcvPhylo	vcvPhylo
write.simmap	write.simmap
writeAncestors	writeAncestors
writeNexus	writeNexus
