phytools-package	phytools-package
add.color.bar	add.color.bar
add.everywhere	add.everywhere
add.random	add.random
allFurcTrees	allFurcTrees
anc.Bayes	anc.Bayes
anc.ML	anc.ML
anc.trend	anc.trend
ancThresh	ancThresh
applyBranchLengths	applyEdgeLengths
ave.rates	ave.rates
bind.tip	bind.tip
bmPlot	bmPlot
branching.diffusion	branching.diffusion
brownie.lite	brownie.lite
brownieREML	brownieREML
contMap	contMap
countSimmap	countSimmap
densityMap	densityMap
describe.simmap	describe.simmap
drop.clade	drop.clade
drop.tip.simmap	drop.tip.simmap
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.strahlerNumber	strahlerNumber
fancyTree	fancyTree
fastAnc	fastAnc
fastBM	fastBM
fastMRCA	fastMRCA
findMRCA	findMRCA
fitBayes	fitBayes
fitDiversityModel	fitDiversityModel
gammatest	gammatest
getDescendants	getDescendants
getExtant	getExtant
getExtinct	getExtant
getSisters	getSisters
getStates	getStates
lambda.transform	lambda.transform
likMlambda	likMlambda
ls.tree	ls.tree
ltt	ltt
ltt95	ltt95
make.era.map	make.era.map
make.simmap	make.simmap
map.overlap	map.overlap
matchNodes	matchNodes
minSplit	minSplit
mrp.supertree	mrp.supertree
multi.mantel	multi.mantel
multiC	multiC
nodeHeights	nodeHeights
optim.phylo.ls	optim.phylo.ls
orderMappedEdge	orderMappedEdge
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
phyloDesign	phyloDesign
phylomorphospace	phylomorphospace
phylomorphospace3d	phylomorphospace3d
phylosig	phylosig
phytools	phytools-package
plotBranchbyTrait	plotBranchbyTrait
plotSimmap	plotSimmap
plotThresh	plotThresh
plotTree	plotTree
posterior.evolrate	posterior.evolrate
ratebystate	ratebystate
read.newick	read.newick
read.simmap	read.simmap
reorderSimmap	reorderSimmap
repPhylo	repPhylo
reroot	reroot
rerootingMethod	rerootingMethod
rescaleSimmap	rescaleSimmap
roundBranches	roundBranches
rstate	rstate
sampleFrom	sampleFrom
sim.corrs	sim.corrs
sim.history	sim.history
sim.ratebystate	sim.ratebystate
sim.rates	sim.rates
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
xkcdTree	xkcdTree
