phangorn-package	phangorn-package
acctran	parsimony
acgt2ry	phyDat
add.tips	add.tips
addConfidences	addConfidences
addTrivialSplits	as.splits
AICc	modelTest
allCircularSplits	as.splits
allDescendants	Ancestors
allSitePattern	phyDat
allSplits	as.splits
allTrees	allTrees
Ancestors	Ancestors
ancestral.pars	ancestral.pml
ancestral.pml	ancestral.pml
as.AAbin.phyDat	phyDat
as.bitsplits.splits	as.splits
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.MultipleAlignment	phyDat
as.MultipleAlignment.phyDat	phyDat
as.networx	as.networx
as.networx.phylo	as.networx
as.networx.splits	as.networx
as.phyDat	phyDat
as.phyDat.alignment	phyDat
as.phyDat.character	phyDat
as.phyDat.data.frame	phyDat
as.phyDat.DNAbin	phyDat
as.phyDat.factor	phyDat
as.phyDat.matrix	phyDat
as.phyDat.MultipleAlignment	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
c.splits	as.splits
cbind.phyDat	phyDat
Children	Ancestors
chloroplast	chloroplast
CI	CI
cladePar	cladePar
coalSpeciesTree	coalSpeciesTree
codon2dna	phyDat
compatible	as.splits
consensusNet	consensusNet
coords	phangorn-internal
cophenetic.networx	cophenetic.networx
cophenetic.splits	cophenetic.networx
createLabel	addConfidences
delta.score	delta.score
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
distinct.splits	as.splits
diversity	getClans
dna2codon	phyDat
edQt	pml.fit
fhm	hadamard
fitch	parsimony
genlight2phyDat	phyDat
getClans	getClans
getClips	getClans
getDiversity	getClans
getRoot	midpoint
getSlices	getClans
h2st	hadamard
h4st	hadamard
hadamard	hadamard
identify.networx	identify.networx
image.phyDat	phyDat
KF.dist	treedist
Laurasiatherian	Laurasiatherian
ldfactorial	dfactorial
lento	lento
lli	pml.fit
map_duplicates	phangorn-internal
mast	mast
matchSplits	as.splits
maxCladeCred	maxCladeCred
midpoint	midpoint
midpoint.multiPhylo	midpoint
midpoint.phylo	midpoint
modelTest	modelTest
mrca.phylo	Ancestors
multiphyDat2pmlPart	pmlPart
neighborNet	neighborNet
networx	as.networx
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
path.dist	treedist
phangorn	phangorn-package
phangorn-internal	phangorn-internal
phyDat	phyDat
phyDat2alignment	phyDat
phyDat2MultipleAlignment	phyDat
plot.networx	as.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	NJ
pratchet	parsimony
presenceAbsence	addConfidences
print.splits	as.splits
pruneTree	midpoint
random.addition	parsimony
read.aa	read.aa
read.nexus.networx	read.nexus.splits
read.nexus.splits	read.nexus.splits
read.phyDat	phyDat
readDist	writeDist
removeTrivialSplits	as.splits
removeUndeterminedSites	phyDat
RF.dist	treedist
RI	CI
rNNI	nni
rSPR	nni
sankoff	parsimony
SH.test	SH.test
Siblings	Ancestors
simSeq	simSeq
simSeq.phylo	simSeq
simSeq.pml	simSeq
SOWH.test	SOWH.test
splits	as.splits
splitsNetwork	splitsNetwork
SPR.dist	treedist
sprdist	treedist
subset.phyDat	phyDat
superTree	superTree
threshStateC	phangorn-internal
treedist	treedist
unique.dist	writeDist
unique.phyDat	phyDat
unique.splits	as.splits
UNJ	NJ
upgma	upgma
wpgma	upgma
wRF.dist	treedist
write.nexus.dist	writeDist
write.nexus.networx	read.nexus.splits
write.nexus.splits	read.nexus.splits
write.phyDat	phyDat
write.splits	read.nexus.splits
writeDist	writeDist
yeast	yeast
