AddTip	AddTip
AllAncestors	AllAncestors
AllDescendantEdges	DescendantEdges
AllSplitPairings	AllSplitPairings
AllSPR	AllSPR
AllTBR	TBR
AncestorEdge	AncestorEdge
ApeTime	ApeTime
AsBinary	AsBinary
brewer	brewer
CladeSizes	CladeSizes
Cladewise	Cladewise
CollapseEdge	CollapseNode
CollapseNode	CollapseNode
congreveLamsdellMatrices	congreveLamsdellMatrices
ConsensusWithout	ConsensusWithout
C_MorphyLength	MorphyTreeLength
C_node_depth	C_node_depth
DescendantEdges	DescendantEdges
DoubleFactorial	DoubleFactorial
doubleFactorials	doubleFactorials
DoubleNNI	DoubleNNI
DropSingleSplits	DropSingleSplits
EdgeAncestry	EdgeAncestry
EdgeListSearch	TreeSearch
EnforceOutgroup	EnforceOutgroup
Entropy	Entropy
Evaluate	Evaluate
ExtractTaxa	ExtractTaxa
Fitch	Fitch
FitchSteps	FitchSteps
ForestSplits	SplitFrequency
GetMorphyLength	MorphyTreeLength
IC1Spr	N1Spr
ICPerStep	ICPerStep
ICS	ICPerStep
ICSteps	ICSteps
inapplicable.citations	inapplicable.citations
inapplicable.datasets	inapplicable.datasets
inapplicable.phyData	inapplicable.phyData
InfoAmounts	InfoAmounts
IWBootstrap	MorphyBootstrap
IWDestroyMorphy	IWScore
IWInitMorphy	IWScore
IWMultiRatchet	Ratchet
IWRatchet	Ratchet
IWRatchetConsensus	Ratchet
IWScore	IWScore
IWScoreMorphy	ProfileScore
IWTreeSearch	TreeSearch
Jackknife	Ratchet
JointInformation	JointInformation
ListToMatrix	ListToMatrix
LnRooted	NRooted
LnSplitMatchProbability	SplitMatchProbability
LnUnrooted	NRooted
LnUnrootedMult	NRooted
LnUnrootedSplits	NRooted
Lobo.data	Lobo.data
Lobo.phy	Lobo.phy
LogDoubleFactorial	DoubleFactorial
LogDoubleFactorial.int	DoubleFactorial
logDoubleFactorials	logDoubleFactorials
LogisticPoints	LogisticPoints
LogTreesConsistentWithTwoSplits	SplitMutualInformation
LogTreesMatchingSplit	TreesMatchingSplit
MarkMissing	ConsensusWithout
MatrixToList	MatrixToList
MatrixToPhyDat	MatrixToPhyDat
MinimumSteps	MinimumSteps
MorphyBootstrap	MorphyBootstrap
MorphyErrorCheck	MorphyErrorCheck
MorphyLength	MorphyTreeLength
MorphyTreeLength	MorphyTreeLength
MorphyWeights	MorphyWeights
mpl_apply_tipdata	mpl_apply_tipdata
mpl_attach_rawdata	mpl_attach_rawdata
mpl_attach_symbols	mpl_attach_symbols
mpl_delete_Morphy	mpl_delete_Morphy
mpl_delete_rawdata	mpl_delete_rawdata
mpl_first_down_recon	mpl_first_down_recon
mpl_first_up_recon	mpl_first_up_recon
mpl_get_charac_weight	mpl_get_charac_weight
mpl_get_numtaxa	mpl_get_numtaxa
mpl_get_num_charac	mpl_get_num_charac
mpl_get_num_internal_nodes	mpl_get_num_internal_nodes
mpl_get_symbols	mpl_get_symbols
mpl_init_Morphy	mpl_init_Morphy
mpl_new_Morphy	mpl_new_Morphy
mpl_second_down_recon	mpl_second_down_recon
mpl_second_up_recon	mpl_second_up_recon
mpl_set_charac_weight	mpl_set_charac_weight
mpl_set_num_internal_nodes	mpl_set_num_internal_nodes
mpl_set_parsim_t	mpl_set_parsim_t
mpl_translate_error	mpl_translate_error
mpl_update_lower_root	mpl_update_lower_root
mpl_update_tip	mpl_update_tip
MultiRatchet	Ratchet
MultiSplitInformation	SplitInformation
MutualArborealInfo	MutualArborealInfo
MutualArborealInfoSplits	MutualArborealInfo
MutualClusterInfo	MutualArborealInfo
MutualClusterInfoSplits	MutualArborealInfo
N1Spr	N1Spr
NewickTree	NewickTree
NeworderPhylo	NeworderPhylo
NeworderPruningwise	NeworderPruningwise
NJTree	NJTree
NNI	NNI
NNISwap	NNI
NonDuplicateRoot	NonDuplicateRoot
NPartitionPairs	NPartitionPairs
NRooted	NRooted
NUnrooted	NRooted
NUnrootedMult	NRooted
NUnrootedSplits	NRooted
OrderEdgesNumberNodes	OrderEdgesNumberNodes
PhyDat	ReadCharacters
PhyDat2Morphy	PhyDat2Morphy
PhyToString	PhyToString
Postorder	Cladewise
PostorderEdges	Cladewise
Preorder	Cladewise
PrepareDataIW	PrepareDataProfile
PrepareDataProfile	PrepareDataProfile
ProfileBootstrap	MorphyBootstrap
ProfileDestroyMorphy	ProfileScore
ProfileInitMorphy	ProfileScore
ProfileRatchet	Ratchet
ProfileScore	ProfileScore
ProfileScoreMorphy	ProfileScore
ProfileTreeSearch	TreeSearch
Pruningwise	Cladewise
RandomMorphyTree	RandomMorphyTree
RandomTree	RandomTree
RandomTreeScore	RandomTreeScore
Ratchet	Ratchet
RatchetConsensus	Ratchet
ReadAsPhyDat	ReadCharacters
ReadCharacters	ReadCharacters
ReadTntAsPhyDat	ReadCharacters
ReadTntCharacters	ReadCharacters
ReadTntTree	ReadTntTree
RearrangeEdges	RearrangeEdges
referenceTree	referenceTree
Renumber	Renumber
RenumberEdges	RenumberTree
RenumberTips	RenumberTips
RenumberTree	RenumberTree
RightmostCharacter	RightmostCharacter
RootedNNI	NNI
RootedNNISwap	NNI
RootedSPR	SPR
RootedSPRSwap	SPR
RootedTBR	TBR
RootedTBRSwap	TBR
RootTree	RootTree
SampleOne	SampleOne
SetMorphyWeights	SetMorphyWeights
SingleCharMorphy	SingleCharMorphy
SingleTaxonTree	SingleTaxonTree
SortTree	SortTree
SplitEntropy	SplitEntropy
SplitFrequency	SplitFrequency
SplitInformation	SplitInformation
SplitMatchProbability	SplitMatchProbability
SplitMutualInformation	SplitMutualInformation
SplitNumber	SplitFrequency
SplitPairingInformationIndex	AllSplitPairings
SplitsCompatible	SplitsCompatible
SplitsRepeated	SplitsRepeated
SplitVariationOfInformation	SplitMutualInformation
SPR	SPR
SPRSwap	SPR
SPRWarning	TBRWarning
StringToPhyDat	StringToPhyDat
StringToPhydat	StringToPhyDat
Suboptimality	Suboptimality
Subtree	Subtree
SuccessiveApproximations	SuccessiveApproximations
SuccessiveWeights	SuccessiveWeights
summary.morphyPtr	summary.morphyPtr
SupportColor	SupportColour
SupportColour	SupportColour
TBR	TBR
TBRMoves	TBR
TBRSwap	TBR
TBRWarning	TBRWarning
TipsAreColumns	TipsAreNames
TipsAreNames	TipsAreNames
TNTText2Tree	ReadTntTree
Tree2Bipartitions	Tree2Splits
Tree2Splits	Tree2Splits
TreesConsistentWithTwoSplits	SplitMutualInformation
TreeSearch	TreeSearch
TreesMatchingSplit	TreesMatchingSplit
TreeSplits	SplitFrequency
UniqueExceptHits	UniqueExceptHits
UniqueSplits	UniqueSplits
UnloadMorphy	UnloadMorphy
UnloadTreeSearch	UnloadTreeSearch
UnrootedTreesMatchingSplit	UnrootedTreesMatchingSplit
VariationOfArborealInfo	MutualArborealInfo
VariationOfArborealInfoSplits	MutualArborealInfo
WithOneExtraStep	WithOneExtraStep
