phangorn-package	phangorn-package
acctran	parsimony
acgt2ry	as.phyDat
add.tips	add.tips
addConfidences	addConfidences
addConfidences.phylo	addConfidences
addTrivialSplits	as.splits
add_boxplot	add_ci
add_ci	add_ci
add_edge_length	add_edge_length
add_mutations	plot.ancestral
add_support	plotBS
AICc	modelTest
allCircularSplits	as.splits
allCompat	maxCladeCred
allDescendants	Ancestors
allSitePattern	phyDat
allSplits	as.splits
allTrees	allTrees
Ancestors	Ancestors
ancestral.pars	ancestral.pml
ancestral.pml	ancestral.pml
anc_pars	ancestral.pml
anc_pml	ancestral.pml
anova.pml	pml
as.AAbin.phyDat	as.phyDat
as.ancestral	write.ancestral
as.bitsplits.splits	as.splits
as.character.phyDat	as.phyDat
as.data.frame.ancestral	ancestral.pml
as.data.frame.phyDat	as.phyDat
as.DNAbin.phyDat	as.phyDat
as.Matrix	as.splits
as.Matrix.splits	as.splits
as.matrix.splits	as.splits
as.MultipleAlignment	as.phyDat
as.MultipleAlignment.phyDat	as.phyDat
as.networx	as.networx
as.networx.phylo	as.networx
as.networx.splits	as.networx
as.phyDat	as.phyDat
as.phyDat.AAbin	as.phyDat
as.phyDat.AAStringSet	as.phyDat
as.phyDat.alignment	as.phyDat
as.phyDat.ancestral	ancestral.pml
as.phyDat.character	as.phyDat
as.phyDat.data.frame	as.phyDat
as.phyDat.DNAbin	as.phyDat
as.phyDat.DNAStringSet	as.phyDat
as.phyDat.factor	as.phyDat
as.phyDat.matrix	as.phyDat
as.phyDat.MultipleAlignment	as.phyDat
as.phylo.splits	as.splits
as.pml	pml
as.prop.part.splits	as.splits
as.splits	as.splits
as.splits.bitsplits	as.splits
as.splits.multiPhylo	as.splits
as.splits.networx	as.splits
as.splits.phylo	as.splits
as.StringSet	as.phyDat
as.StringSet.phyDat	as.phyDat
bab	bab
baseFreq	baseFreq
bootstrap.phyDat	bootstrap.pml
bootstrap.pml	bootstrap.pml
BranchAndBound	bab
c.phyDat	phyDat
c.splits	as.splits
candidate_tree	phangorn-internal
cbind.phyDat	phyDat
Children	Ancestors
chloroplast	chloroplast
CI	CI
cladePar	cladePar
coalSpeciesTree	coalSpeciesTree
codon2dna	dna2codon
codonTest	codonTest
compatible	as.splits
composition_test	baseFreq
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.beta	discrete.gamma
discrete.gamma	discrete.gamma
dist.hamming	dist.hamming
dist.logDet	dist.hamming
dist.ml	dist.hamming
dist.p	dist.p
distanceHadamard	distanceHadamard
distinct.splits	as.splits
diversity	getClans
dna2aa	dna2codon
dna2codon	dna2codon
edQt	pml.fit
fhm	hadamard
fitch	parsimony
gap_as_ambiguous	gap_as_state
gap_as_state	gap_as_state
genlight2phyDat	as.phyDat
getClans	getClans
getClips	getClans
getDiversity	getClans
getRoot	midpoint
getSlices	getClans
glance	reexports
glance.phyDat	baseFreq
h2st	hadamard
h4st	hadamard
hadamard	hadamard
hash	phangorn-internal
has_gap_state	gap_as_state
identify.networx	identify.networx
image.phyDat	image.phyDat
keep_as_tip	midpoint
KF.dist	treedist
latag2n.phyDat	latag2n.phyDat
Laurasiatherian	Laurasiatherian
ldfactorial	dfactorial
lento	lento
lli	pml.fit
logLik.pml	pml
map_duplicates	phangorn-internal
mast	mast
matchSplits	as.splits
maxCladeCred	maxCladeCred
mcc	maxCladeCred
midpoint	midpoint
midpoint.multiPhylo	midpoint
midpoint.phylo	midpoint
mites	mites
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	as.phyDat
phyDat2alignment	as.phyDat
phyDat2MultipleAlignment	as.phyDat
plot.networx	plot.networx
plot.pml	plot.pml
plotAnc	plot.ancestral
plotBS	plotBS
plotRates	discrete.gamma
plotSeqLogo	plot.ancestral
plot_gamma_plus_inv	discrete.gamma
pml	pml
pml.control	pml.control
pml.fit	pml.fit
pml.free	pml.fit
pml.init	pml.fit
pmlCluster	pmlCluster
pmlMix	pmlMix
pmlPart	pmlPart
pmlPart2multiPhylo	pmlPart
pmlPen	phangorn-internal
pml_bb	pml_bb
pratchet	parsimony
presenceAbsence	addConfidences
print.ancestral	write.ancestral
print.phyDat	phyDat
print.pml	pml
print.splits	as.splits
pruneTree	midpoint
random.addition	parsimony
ratchet.control	pml.control
read.nexus.dist	writeDist
read.nexus.networx	read.nexus.splits
read.nexus.partitions	read.nexus.partitions
read.nexus.splits	read.nexus.splits
read.phyDat	read.phyDat
readDist	writeDist
reexports	reexports
removeAmbiguousSites	phyDat
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
summary.clanistics	getClans
superTree	superTree
supgma	upgma
threshStateC	phangorn-internal
tidy	reexports
transferBootstrap	transferBootstrap
treedist	treedist
unique.dist	writeDist
unique.phyDat	phyDat
unique.splits	as.splits
UNJ	NJ
upgma	upgma
vcov.pml	pml
wpgma	upgma
wRF.dist	treedist
write.ancestral	write.ancestral
write.nexus.dist	writeDist
write.nexus.networx	read.nexus.splits
write.nexus.splits	read.nexus.splits
write.phyDat	read.phyDat
write.pml	write.pml
write.splits	read.nexus.splits
writeDist	writeDist
yeast	yeast
[.phyDat	phyDat
