TreeTools-package	TreeTools-package
%in%,multiPhylo,multiPhylo-method	match.multiPhylo
%in%,multiPhylo,phylo-method	match.multiPhylo
%in%,phylo,multiPhylo-method	match.multiPhylo
%in%,phylo,phylo-method	match.multiPhylo
%in%,Splits,Splits-method	match.Splits
.CompatibleRaws	CompatibleSplits
.CompatibleSplit	CompatibleSplits
.RandomParent	dot-RandomParent
.UnrootedKeys	TreeShape
<.MixedBase	sort.multiPhylo
<.phylo	sort.multiPhylo
==.MixedBase	sort.multiPhylo
==.phylo	sort.multiPhylo
>.MixedBase	sort.multiPhylo
>.phylo	sort.multiPhylo
AddTip	AddTip
AddTipEverywhere	AddTip
AddUnconstrained	ImposeConstraint
AllAncestors	ListAncestors
AllTipLabels	TipLabels
AllTipLabels.list	TipLabels
AllTipLabels.matrix	TipLabels
AllTipLabels.multiPhylo	TipLabels
AllTipLabels.phylo	TipLabels
AllTipLabels.Splits	TipLabels
AllTipLabels.TreeNumber	TipLabels
AncestorEdge	AncestorEdge
ApePostorder	Reorder
ApePostorder.list	Reorder
ApePostorder.multiPhylo	Reorder
ApePostorder.NULL	Reorder
ApePostorder.phylo	Reorder
ApeTime	ApeTime
ArtEx	ArtificialExtinction
ArtificialExtinction	ArtificialExtinction
ArtificialExtinction.matrix	ArtificialExtinction
ArtificialExtinction.phyDat	ArtificialExtinction
as.ClusterTable	ClusterTable
as.ClusterTable.list	ClusterTable
as.ClusterTable.multiPhylo	ClusterTable
as.ClusterTable.phylo	ClusterTable
as.logical.Splits	Splits
as.matrix.ClusterTable	ClusterTable-methods
as.MixedBase	TreeNumber
as.MixedBase.integer64	TreeNumber
as.MixedBase.MixedBase	TreeNumber
as.MixedBase.multiPhylo	TreeNumber
as.MixedBase.numeric	TreeNumber
as.MixedBase.phylo	TreeNumber
as.MixedBase.TreeNumber	TreeNumber
as.multiPhylo	as.multiPhylo
as.multiPhylo.list	as.multiPhylo
as.multiPhylo.phyDat	as.multiPhylo
as.multiPhylo.phylo	as.multiPhylo
as.multiPhylo.Splits	as.multiPhylo
as.Newick	as.Newick
as.Newick.list	as.Newick
as.Newick.multiPhylo	as.Newick
as.Newick.phylo	as.Newick
as.phylo.MixedBase	TreeNumber
as.phylo.numeric	TreeNumber
as.phylo.TreeNumber	TreeNumber
as.Splits	Splits
as.Splits.character	Splits
as.Splits.integer	Splits
as.Splits.list	Splits
as.Splits.logical	Splits
as.Splits.matrix	Splits
as.Splits.multiPhylo	Splits
as.Splits.numeric	Splits
as.Splits.phylo	Splits
as.Splits.Splits	Splits
as.TreeNumber	TreeNumber
as.TreeNumber.character	TreeNumber
as.TreeNumber.MixedBase	TreeNumber
as.TreeNumber.multiPhylo	TreeNumber
as.TreeNumber.phylo	TreeNumber
as.TreeNumber.TreeNumber	TreeNumber
BalancedTree	GenerateTree
brewer	brewer
CharacterInformation	CharacterInformation
Cherries	Cherries
Cherries.numeric	Cherries
Cherries.phylo	Cherries
CladeSizes	CladeSizes
Cladewise	Reorder
Cladewise.list	Reorder
Cladewise.matrix	Reorder
Cladewise.multiPhylo	Reorder
Cladewise.NULL	Reorder
Cladewise.phylo	Reorder
CladisticInfo	CladisticInfo
CladisticInfo.list	CladisticInfo
CladisticInfo.multiPhylo	CladisticInfo
CladisticInfo.phylo	CladisticInfo
CladisticInfo.Splits	CladisticInfo
CladisticInformation	CladisticInfo
ClusterTable	ClusterTable
ClusterTable-methods	ClusterTable-methods
CollapseEdge	CollapseNode
CollapseNode	CollapseNode
CollapseNode.phylo	CollapseNode
CompatibleSplits	CompatibleSplits
Consensus	Consensus
ConsensusWithout	ConsensusWithout
ConsensusWithout.list	ConsensusWithout
ConsensusWithout.multiPhylo	ConsensusWithout
ConsensusWithout.phylo	ConsensusWithout
ConstrainedNJ	ConstrainedNJ
Decompose	Decompose
DescendantEdges	DescendantEdges
DescendantTips	DescendantEdges
DoubleFactorial	DoubleFactorial
DoubleFactorial64	DoubleFactorial
doubleFactorials	doubleFactorials
DropTip	DropTip
DropTip.list	DropTip
DropTip.multiPhylo	DropTip
DropTip.NULL	DropTip
DropTip.phylo	DropTip
DropTip.Splits	DropTip
DropTipPhylo	DropTip
EdgeAncestry	EdgeAncestry
EdgeDistances	EdgeDistances
EdgeRatio	EdgeRatio
EdgeRatio.phylo	EdgeRatio
edge_to_splits	edge_to_splits
EndSentence	EndSentence
ExtractTaxa	ExtractTaxa
FirstMatchingSplit	match.Splits
GenerateTree	GenerateTree
Hamming	Hamming
IC1Spr	N1Spr
ImposeConstraint	ImposeConstraint
is.TreeNumber	is.TreeNumber
J1Index	J1Index
JQIndex	J1Index
KeepTip	DropTip
KeepTip.list	DropTip
KeepTip.multiPhylo	DropTip
KeepTip.NULL	DropTip
KeepTip.phylo	DropTip
KeepTip.Splits	DropTip
KeepTipPostorder	DropTip
KeepTipPreorder	DropTip
KeptPaths	KeptPaths
KeptPaths.data.frame	KeptPaths
KeptPaths.matrix	KeptPaths
KeptVerts	KeptVerts
KeptVerts.numeric	KeptVerts
KeptVerts.phylo	KeptVerts
LabelSplits	LabelSplits
LeafLabelInterchange	LeafLabelInterchange
ListAncestors	ListAncestors
LnDoubleFactorial	DoubleFactorial
LnDoubleFactorial.int	DoubleFactorial
LnRooted	NRooted
LnRooted.int	NRooted
LnSplitMatchProbability	SplitMatchProbability
LnTreesMatchingSplit	TreesMatchingSplit
LnTreesMatchingTree	TreesMatchingTree
LnUnrooted	NRooted
LnUnrooted.int	NRooted
LnUnrootedMult	NRooted
LnUnrootedSplits	NRooted
LnUnrootedTreesMatchingSplit	UnrootedTreesMatchingSplit
Lobo.data	Lobo.data
Lobo.phy	Lobo.data
Log2DoubleFactorial	DoubleFactorial
Log2Rooted	NRooted
Log2Rooted.int	NRooted
Log2TreesMatchingSplit	TreesMatchingSplit
Log2TreesMatchingTree	TreesMatchingTree
Log2Unrooted	NRooted
Log2Unrooted.int	NRooted
Log2UnrootedMult	NRooted
Log2UnrootedSplits	NRooted
Log2UnrootedTreesMatchingSplit	UnrootedTreesMatchingSplit
LogDoubleFactorial	DoubleFactorial
LogDoubleFactorial.int	DoubleFactorial
logDoubleFactorials	logDoubleFactorials
LongBranch	LongBranch
MakeTreeBinary	MakeTreeBinary
MarkMissing	ConsensusWithout
match	match.Splits
match,multiPhylo,multiPhylo-method	match.multiPhylo
match,multiPhylo,phylo-method	match.multiPhylo
match,phylo,multiPhylo-method	match.multiPhylo
match,phylo,phylo-method	match.multiPhylo
match,Splits,Splits-method	match.Splits
MatchEdges	MatchEdges
MatchNodes	MatchEdges
MatchStrings	MatchStrings
MatrixToPhyDat	MatrixToPhyDat
MorphoBankDecode	MorphoBankDecode
MrBayesTrees	ReadMrBayesTrees
MRCA	MRCA
MSTEdges	MSTEdges
MSTLength	MSTEdges
MultiSplitInformation	SplitInformation
N1Spr	N1Spr
NDescendants	NDescendants
NewickTree	NewickTree
Neworder	Neworder
NeworderPhylo	Neworder
NeworderPruningwise	Neworder
NexusTokens	ExtractTaxa
NexusTokensToInteger	NexusTokensToInteger
NJTree	NJTree
NodeDepth	NodeDepth
NodeNumbers	NodeNumbers
NodeOrder	NodeOrder
NPartitionPairs	NPartitionPairs
NPartitions	NSplits
NRooted	NRooted
NRooted64	NRooted
NRootedShapes	TreeShape
nRootedShapes	nRootedShapes
NSplits	NSplits
NSplits.character	NSplits
NSplits.ClusterTable	NSplits
NSplits.list	NSplits
NSplits.multiPhylo	NSplits
NSplits.NULL	NSplits
NSplits.numeric	NSplits
NSplits.phylo	NSplits
NSplits.Splits	NSplits
NTip	NTip
NTip.default	NTip
NTip.list	NTip
NTip.matrix	NTip
NTip.multiPhylo	NTip
NTip.phyDat	NTip
NTip.phylo	NTip
NTip.Splits	NTip
NUnrooted	NRooted
NUnrooted64	NRooted
NUnrootedMult	NRooted
NUnrootedShapes	TreeShape
nUnrootedShapes	nRootedShapes
NUnrootedSplits	NRooted
PaintTree	PaintTree
PairwiseDistances	PairwiseDistances
PathLengths	PathLengths
PectinateTree	GenerateTree
PhyDat	ReadCharacters
PhyDatToMatrix	MatrixToPhyDat
PhyDatToString	PhyToString
PhydatToString	PhyToString
PhyToString	PhyToString
PolarizeSplits	PolarizeSplits
Postorder	Reorder
Postorder.list	Reorder
Postorder.multiPhylo	Reorder
Postorder.NULL	Reorder
Postorder.numeric	Reorder
Postorder.phylo	Reorder
PostorderOrder	Reorder
PostorderOrder.numeric	Reorder
PostorderOrder.phylo	Reorder
Preorder	Reorder
Preorder.list	Reorder
Preorder.multiPhylo	Reorder
Preorder.NULL	Reorder
Preorder.numeric	Reorder
Preorder.phylo	Reorder
print.ClusterTable	ClusterTable-methods
print.TreeNumber	print.TreeNumber
Pruningwise	Reorder
Pruningwise.list	Reorder
Pruningwise.multiPhylo	Reorder
Pruningwise.NULL	Reorder
Pruningwise.phylo	Reorder
RandomTree	GenerateTree
ReadAsPhyDat	ReadCharacters
ReadCharacters	ReadCharacters
ReadMrBayes	ReadMrBayesTrees
ReadMrBayesTrees	ReadMrBayesTrees
ReadNotes	ReadCharacters
ReadTNTAsPhyDat	ReadCharacters
ReadTntAsPhyDat	ReadCharacters
ReadTNTCharacters	ReadCharacters
ReadTntCharacters	ReadCharacters
ReadTntTree	ReadTntTree
Renumber	Renumber
RenumberEdges	Reorder
RenumberTips	RenumberTips
RenumberTips.list	RenumberTips
RenumberTips.multiPhylo	RenumberTips
RenumberTips.NULL	RenumberTips
RenumberTips.phylo	RenumberTips
RenumberTips.Splits	RenumberTips
RenumberTree	Reorder
Reorder	Reorder
replicate64	sapply64
Reweight	Reweight
RightmostCharacter	RightmostCharacter
RoguePlot	RoguePlot
RootedTreeShape	TreeShape
RootedTreeWithShape	TreeShape
RootNode	RootNode
RootNodeDist	Stemwardness
RootNodeDistance	Stemwardness
RootNodeDistance.character	Stemwardness
RootNodeDistance.numeric	Stemwardness
RootOnNode	RootTree
RootTree	RootTree
root_on_node	root_on_node
SampleOne	SampleOne
sapply64	sapply64
SingleTaxonTree	TrivialTree
SisterSize	Stemwardness
SisterSize.character	Stemwardness
SisterSize.numeric	Stemwardness
sort.multiPhylo	sort.multiPhylo
SortTree	SortTree
SortTree.list	SortTree
SortTree.multiPhylo	SortTree
SortTree.phylo	SortTree
SplitConflicts	SplitConsistent
SplitConsistent	SplitConsistent
SplitFrequency	SplitFrequency
SplitImbalance	TipsInSplits
SplitImbalance.phylo	TipsInSplits
SplitImbalance.Splits	TipsInSplits
SplitInformation	SplitInformation
SplitInformation.numeric	SplitInformation
SplitInformation.phylo	SplitInformation
SplitInformation.Splits	SplitInformation
SplitMatchProbability	SplitMatchProbability
Splits	Splits
SplitsInBinaryTree	SplitsInBinaryTree
SplitsInBinaryTree.default	SplitsInBinaryTree
SplitsInBinaryTree.list	SplitsInBinaryTree
SplitsInBinaryTree.multiPhylo	SplitsInBinaryTree
SplitsInBinaryTree.NULL	SplitsInBinaryTree
SplitsInBinaryTree.numeric	SplitsInBinaryTree
SplitsInBinaryTree.phylo	SplitsInBinaryTree
SplitsInBinaryTree.Splits	SplitsInBinaryTree
StarTree	GenerateTree
Stemminess	Treeness
Stemwardness	Stemwardness
StringToPhyDat	PhyToString
StringToPhydat	PhyToString
Subsplit	Subsplit
Subtree	Subtree
summary.ClusterTable	ClusterTable-methods
SupportColor	SupportColour
SupportColour	SupportColour
TCIContext	TotalCopheneticIndex
TCIContext.numeric	TotalCopheneticIndex
TipLabels	TipLabels
TipLabels.character	TipLabels
TipLabels.default	TipLabels
TipLabels.list	TipLabels
TipLabels.logical	TipLabels
TipLabels.matrix	TipLabels
TipLabels.MixedBase	TipLabels
TipLabels.multiPhylo	TipLabels
TipLabels.numeric	TipLabels
TipLabels.phyDat	TipLabels
TipLabels.phylo	TipLabels
TipLabels.Splits	TipLabels
TipLabels.TreeNumber	TipLabels
TipsInSplits	TipsInSplits
TipsInSplits.phylo	TipsInSplits
TipsInSplits.Splits	TipsInSplits
TipTimedTree	TipTimedTree
TNTOrder	Reorder
TntOrder	Reorder
TntOrder.list	Reorder
TntOrder.multiPhylo	Reorder
TntOrder.NULL	Reorder
TntOrder.numeric	Reorder
TntOrder.phylo	Reorder
TNTText2Tree	ReadTntTree
TntText2Tree	ReadTntTree
TopologyOnly	TopologyOnly
TotalCopheneticIndex	TotalCopheneticIndex
TreeIsRooted	TreeIsRooted
Treeness	Treeness
TreeNumber	TreeNumber
TreeShape	TreeShape
TreesMatchingSplit	TreesMatchingSplit
TreesMatchingTree	TreesMatchingTree
TreeTools	TreeTools-package
TrivialSplits	TrivialSplits
TrivialTree	TrivialTree
Unquote	Unquote
UnrootedKeys	TreeShape
unrootedKeys	TreeShape
UnrootedTreeKey	TreeShape
UnrootedTreeShape	TreeShape
UnrootedTreesMatchingSplit	UnrootedTreesMatchingSplit
UnrootedTreeWithKey	TreeShape
UnrootedTreeWithShape	TreeShape
UnrootTree	RootTree
UnshiftTree	UnshiftTree
vapply64	sapply64
WithoutTrivialSplits	TrivialSplits
WriteTntCharacters	WriteTntCharacters
WriteTntCharacters.matrix	WriteTntCharacters
WriteTntCharacters.phyDat	WriteTntCharacters
xor	xor
xor,Splits,Splits-method	xor
YuleTree	GenerateTree
ZeroTaxonTree	TrivialTree
