phangorn-package	phangorn-package
acctran	parsimony
acgt2ry	phyDat
addConfidences	as.splits
addTrivialSplits	as.splits
AICc	modelTest
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	as.splits
as.Matrix.splits	as.splits
as.matrix.splits	as.splits
as.networx	plot.networx
as.networx.splits	plot.networx
as.phyDat	phyDat
as.phyDat.alignment	phyDat
as.phyDat.DNAbin	phyDat
as.phylo.splits	as.splits
as.prop.part.splits	as.splits
as.splits	as.splits
as.splits.multiPhylo	as.splits
as.splits.networx	as.splits
as.splits.phylo	as.splits
bab	bab
baseFreq	phyDat
bootstrap.phyDat	bootstrap.pml
bootstrap.pml	bootstrap.pml
BranchAndBound	bab
c.phyDat	phyDat
cbind.phyDat	phyDat
Children	Ancestors
chloroplast	chloroplast
CI	parsimony
cladePar	cladePar
coalSpeciesTree	superTree
compatible	as.splits
consensusNet	consensusNet
countCycles	as.splits
densiTree	densiTree
Descendants	Ancestors
designSplits	designTree
designTree	designTree
dfactorial	dfactorial
discrete.gamma	pml.fit
dist.hamming	dist.hamming
dist.logDet	dist.hamming
dist.ml	dist.hamming
dist.p	dist.p
distanceHadamard	distanceHadamard
diversity	getClans
edQt	pml.fit
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
lli	pml.fit
midpoint	midpoint
modelTest	modelTest
mrca.phylo	Ancestors
neighborNet	neighborNet
NJ	NJ
nni	nni
nnls.networx	designTree
nnls.phylo	designTree
nnls.splits	designTree
nnls.tree	designTree
optim.parsimony	parsimony
optim.pml	pml
pace	ancestral.pml
parsimony	parsimony
phangorn	phangorn-package
phyDat	phyDat
phyDat2alignment	phyDat
plot.networx	plot.networx
plotAnc	ancestral.pml
plotBS	bootstrap.pml
pml	pml
pml.control	pml
pml.fit	pml.fit
pml.free	pml.fit
pml.init	pml.fit
pmlCluster	pmlCluster
pmlMix	pmlMix
pmlPart	pmlPart
pmlPart2multiPhylo	pmlPart
pmlPen	pmlMix
PNJ	parsimony
pratchet	parsimony
presenceAbsence	as.splits
print.splits	as.splits
pruneTree	midpoint
random.addition	parsimony
read.aa	read.aa
read.nexus.splits	as.splits
read.phyDat	phyDat
readDist	dist.hamming
RF.dist	treedist
RI	parsimony
rNNI	nni
rSPR	nni
sankoff	parsimony
SH.test	SH.test
Siblings	Ancestors
simSeq	simSeq
simSeq.phylo	simSeq
simSeq.pml	simSeq
SOWH.test	SOWH.test
splitsNetwork	splitsNetwork
subset.phyDat	phyDat
superTree	superTree
treedist	treedist
UNJ	NJ
upgma	upgma
wpgma	upgma
write.nexus.splits	as.splits
write.phyDat	phyDat
write.splits	as.splits
writeDist	dist.hamming
yeast	yeast
