ancandtime	ancandtime
ancestor	ancestor
bootstrap	bootstrap
bootstrap.mulgene	bootstrap.mulgene
change.root	change.root
ChangeBrlen	ChangeBrlen
coal.sptree	coal.sptree
coaltime	coaltime
consense	consense
del.node	del.node
FindSpnodeDownGenenode	FindSpnodeDownGenenode
genetree.vector	genetree.vector
getcoaltime	getcoaltime
getncoal	getncoal
is.clock	is.clock
is.rootedtree	is.rootedtree
maxtree	maxtree
mrca.2nodes	mrca.2nodes
mrca.nodes	mrca.nodes
mutation_exp	mutation_exp
name2node	name2node
noclock2clock	noclock2clock
node.height	node.height
node2name	node2name
offspring.nodes	offspring.nodes
offspring.nodes.string	offspring.nodes.string
offspring.species	offspring.species
pair.dist	pair.dist
pair.dist.dna	pair.dist.dna
pair.dist.mulseq	pair.dist.mulseq
partition.tree	partition.tree
PhyBase	phybase-package
plottree	plottree
popsize	popsize
populationMutation	populationMutation
postdist.tree	postdist.tree
rank.nodes	rank.nodes
rannalandyang	rannalandyang
rdirichlet	rdirichlet
read.dna.seq	read.dna.seq
read.tree.nodes	read.tree.nodes
read.tree.string	read.tree.string
root.tree	root.tree
rooted.tree	rooted.tree
rootoftree	rootoftree
sctree	sctree
sim.coaltree	sim.coaltree
sim.coaltree.sp	sim.coaltree.sp
sim.coaltree.sp.mu	sim.coaltree.sp.mu
sim.dna	sim.dna
simnucleotide	simnucleotide
simSeqfromSp	simSeqfromSp
site.pattern	site.pattern
sortmat	sortmat
species.name	species.name
spstructure	spstructure
sptree	sptree
star.sptree	star.sptree
steac.sptree	steac.sptree
subtree	subtree
subtree.length	subtree.length
swap.nodes	swap.nodes
treedist	treedist
tripleloglike	tripleloglike
triplenumber	triplenumber
triplepara	triplepara
tripleProb	tripleProb
unrooted.tree	unrooted.tree
unroottree	unroottree
upgma	upgma
write.dna	write.dna
write.subtree	write.subtree
write.tree.string	write.tree.string
