phangorn-package	phangorn-package
acctran	parsimony
acgt2ry	phyDat
allSitePattern	phyDat
allSplits	as.splits
allTrees	allTrees
Ancestors	Ancestors
ancestral.pars	ancestral.pml
ancestral.pml	ancestral.pml
as.character.phyDat	phyDat
as.data.frame.phyDat	phyDat
as.DNAbin.phyDat	phyDat
as.matrix.splits	as.splits
as.networx	consensusNet
as.networx.splits	consensusNet
as.phyDat	phyDat
as.phyDat.DNAbin	phyDat
as.prop.part	as.splits
as.splits	as.splits
as.splits.multiPhylo	as.splits
as.splits.phylo	as.splits
bab	bab
bootstrap.phyDat	bootstrap.pml
bootstrap.pml	bootstrap.pml
BranchAndBound	bab
Children	Ancestors
chloroplast	chloroplast
CI	parsimony
compatible	as.splits
consensusNet	consensusNet
Descendants	Ancestors
designSplits	designTree
designTree	designTree
dfactorial	dfactorial
dist.hamming	dist.hamming
dist.logDet	dist.hamming
dist.ml	dist.hamming
distanceHadamard	distanceHadamard
fhm	hadamard
fitch	parsimony
getClans	getClans
getClips	getClans
getDiversity	getClans
getRoot	midpoint
getSlices	getClans
h2st	hadamard
h4st	hadamard
hadamard	hadamard
Laurasiatherian	Laurasiatherian
ldfactorial	dfactorial
lento	lento
midpoint	midpoint
modelTest	modelTest
NJ	NJ
nni	nni
nnls.tree	designTree
optim.parsimony	parsimony
optim.pml	pml
pace	ancestral.pml
parsimony	parsimony
phangorn	phangorn-package
phyDat	phyDat
plot.networx	plot.networx
plotAnc	ancestral.pml
plotBS	bootstrap.pml
pml	pml
pml.control	pml
pmlCluster	pmlCluster
pmlMix	pmlMix
pmlPart	pmlPart
pmlPen	pmlMix
PNJ	parsimony
pratchet	parsimony
print.splits	as.splits
pruneTree	midpoint
random.addition	parsimony
read.aa	read.aa
read.phyDat	phyDat
RF.dist	treedist
RI	parsimony
rNNI	nni
rSPR	nni
sankoff	parsimony
SH.test	SH.test
Siblings	Ancestors
simSeq	simSeq
splitsNetwork	splitsNetwork
subset.phyDat	phyDat
treedist	treedist
UNJ	NJ
upgma	upgma
wpgma	upgma
write.nexus.splits	hadamard
write.phyDat	phyDat
write.splits	as.splits
yeast	yeast
