.CombineResults	dot-CombineResults
.GapHandler	dot-GapHandler
.NonDuplicateRoot	dot-NonDuplicateRoot
.ReplaceResults	dot-CombineResults
.UniqueExceptHits	dot-UniqueExceptHits
AdditionTree	AdditionTree
AllSPR	AllSPR
Carter1	Carter1
CharacterLength	CharacterLength
ClusteringConcordance	SiteConcordance
ClusterStrings	ClusterStrings
cNNI	NNI
ConcordantInfo	ConcordantInformation
ConcordantInformation	ConcordantInformation
congreveLamsdellMatrices	congreveLamsdellMatrices
Consistency	Consistency
cSPR	cSPR
C_MorphyLength	MorphyTreeLength
DoNothing	TreeSearch
DoubleNNI	DoubleNNI
EasyTrees	MaximizeParsimony
EasyTreesy	MaximizeParsimony
EdgeListSearch	TreeSearch
EmptyPhyDat	TreeSearch
Evaluate	ConcordantInformation
ExpectedLength	ExpectedLength
FastCharacterLength	CharacterLength
Fitch	TreeLength
FitchSteps	CharacterLength
GapHandler	GapHandler
GetMorphyLength	MorphyTreeLength
inapplicable.citations	inapplicable.datasets
inapplicable.datasets	inapplicable.datasets
inapplicable.phyData	inapplicable.datasets
inapplicable.trees	inapplicable.datasets
is.morphyPtr	is.morphyPtr
IWScore	TreeLength
IWTreeSearch	TreeSearch
Jackknife	Jackknife
JackLabels	JackLabels
LengthAdded	LengthAdded
Log2Carter1	Carter1
LogCarter1	Carter1
MaximizeParsimony	MaximizeParsimony
MaximumLength	MinimumLength
MaximumLength.character	MinimumLength
MaximumLength.numeric	MinimumLength
MinimumLength	MinimumLength
MinimumLength.character	MinimumLength
MinimumLength.numeric	MinimumLength
MinimumLength.phyDat	MinimumLength
MinimumSteps	MinimumLength
MorphyBootstrap	Ratchet
MorphyErrorCheck	MorphyErrorCheck
MorphyLength	MorphyTreeLength
MorphyTreeLength	MorphyTreeLength
MorphyWeights	MorphyWeights
MostContradictedFreq	MostContradictedFreq
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_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_gaphandl	mpl_get_gaphandl
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_gaphandl	mpl_get_gaphandl
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
MutualClusteringConcordance	SiteConcordance
NNI	NNI
NNISwap	NNI
PhyDat2Morphy	PhyDat2Morphy
PhylogeneticConcordance	SiteConcordance
PlotCharacter	PlotCharacter
PlotCharacter.list	PlotCharacter
PlotCharacter.multiPhylo	PlotCharacter
PlotCharacter.phylo	PlotCharacter
PolEscapa	LengthAdded
PrepareDataIW	PrepareDataProfile
PrepareDataProfile	PrepareDataProfile
PresCont	PresCont
profiles	profiles
QuartetConcordance	SiteConcordance
QuartetResolution	QuartetResolution
RandomMorphyTree	RandomMorphyTree
RandomTreeScore	RandomTreeScore
Ratchet	Ratchet
RatchetConsensus	Ratchet
RearrangeEdges	RearrangeEdges
referenceTree	referenceTree
Resample	MaximizeParsimony
RootedNNI	NNI
RootedNNISwap	NNI
RootedSPR	SPR
RootedSPRSwap	SPR
RootedTBR	TBR
RootedTBRSwap	TBR
SetMorphyWeights	MorphyWeights
SharedPhylogeneticConcordance	SiteConcordance
SingleCharMorphy	SingleCharMorphy
SiteConcordance	SiteConcordance
SPR	SPR
SPRMoves	SPR
SPRMoves.matrix	SPR
SPRMoves.phylo	SPR
SPRSwap	SPR
SPRWarning	TBRWarning
StepInformation	StepInformation
StopUnlessBifurcating	StopUnlessBifurcating
Suboptimality	Suboptimality
SuccessiveApproximations	SuccessiveApproximations
SuccessiveWeights	SuccessiveApproximations
summary.morphyPtr	summary.morphyPtr
TaxonInfluence	TaxonInfluence
TBR	TBR
TBRMoves	TBR
TBRMoves.matrix	TBR
TBRMoves.phylo	TBR
TBRSwap	TBR
TBRWarning	TBRWarning
TreeLength	TreeLength
TreeLength.list	TreeLength
TreeLength.multiPhylo	TreeLength
TreeLength.numeric	TreeLength
TreeLength.phylo	TreeLength
TreeSearch	TreeSearch
UnloadMorphy	UnloadMorphy
WhenFirstHit	WhenFirstHit
WithOneExtraStep	WithOneExtraStep
