TreeTools-package	TreeTools-package
%in%	match
%in%.Splits	match
.CompatibleRaws	CompatibleSplits
.CompatibleSplit	CompatibleSplits
.RandomParent	dot-RandomParent
.UnrootedKeys	TreeShape
AddTip	AddTip
AddTipEverywhere	AddTip
AllAncestors	ListAncestors
AllDescendantEdges	DescendantEdges
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.phylo	Reorder
ApeTime	ApeTime
ArtEx	ArtificialExtinction
ArtificialExtinction	ArtificialExtinction
ArtificialExtinction.matrix	ArtificialExtinction
ArtificialExtinction.phyDat	ArtificialExtinction
as.logical.Splits	as.Splits
as.Newick	as.Newick
as.Newick.list	as.Newick
as.Newick.multiPhylo	as.Newick
as.Newick.phylo	as.Newick
as.phylo.numeric	TreeNumber
as.phylo.TreeNumber	TreeNumber
as.Splits	as.Splits
as.Splits.list	as.Splits
as.Splits.logical	as.Splits
as.Splits.matrix	as.Splits
as.Splits.multiPhylo	as.Splits
as.Splits.phylo	as.Splits
as.Splits.Splits	as.Splits
as.TreeNumber	TreeNumber
as.TreeNumber.character	TreeNumber
as.TreeNumber.multiPhylo	TreeNumber
as.TreeNumber.phylo	TreeNumber
BalancedTree	GenerateTree
brewer	brewer
CharacterInformation	CharacterInformation
CladeSizes	CladeSizes
Cladewise	Reorder
Cladewise.list	Reorder
Cladewise.matrix	Reorder
Cladewise.multiPhylo	Reorder
Cladewise.phylo	Reorder
CladisticInfo	CladisticInfo
CladisticInfo.list	CladisticInfo
CladisticInfo.multiPhylo	CladisticInfo
CladisticInfo.phylo	CladisticInfo
CladisticInformation	CladisticInfo
CollapseEdge	CollapseNode
CollapseNode	CollapseNode
CollapseNode.phylo	CollapseNode
CompatibleSplits	CompatibleSplits
ConsensusWithout	ConsensusWithout
ConsensusWithout.list	ConsensusWithout
ConsensusWithout.multiPhylo	ConsensusWithout
ConsensusWithout.phylo	ConsensusWithout
DescendantEdges	DescendantEdges
DoubleFactorial	DoubleFactorial
DoubleFactorial64	DoubleFactorial
doubleFactorials	doubleFactorials
DropTip	DropTip
DropTip.multiPhylo	DropTip
DropTip.phylo	DropTip
EdgeAncestry	EdgeAncestry
EdgeDistances	EdgeDistances
EnforceOutgroup	EnforceOutgroup
EnforceOutgroup.character	EnforceOutgroup
EnforceOutgroup.phylo	EnforceOutgroup
ExtractTaxa	ExtractTaxa
ForestSplits	SplitFrequency
GenerateTree	GenerateTree
IC1Spr	N1Spr
in.Splits	match
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
MakeTreeBinary	MakeTreeBinary
MarkMissing	ConsensusWithout
match	match
match.list	match
match.Splits	match
MatrixToPhyDat	MatrixToPhyDat
MRCA	MRCA
MSTEdges	MSTEdges
MSTLength	MSTEdges
MultiSplitInformation	SplitInformation
N1Spr	N1Spr
NDescendants	NDescendants
NewickTree	NewickTree
Neworder	Neworder
NeworderPhylo	Neworder
NeworderPruningwise	Neworder
NexusTokens	ExtractTaxa
NJTree	NJTree
NodeDepth	NodeDepth
NodeOrder	NodeOrder
NonDuplicateRoot	NonDuplicateRoot
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.phylo	NTip
NTip.Splits	NTip
NUnrooted	NRooted
NUnrooted64	NRooted
NUnrootedMult	NRooted
NUnrootedShapes	TreeShape
nUnrootedShapes	nRootedShapes
NUnrootedSplits	NRooted
PairwiseDistances	PairwiseDistances
PectinateTree	GenerateTree
PhyDat	ReadCharacters
PhyDatToMatrix	MatrixToPhyDat
PhyDatToString	PhyToString
PhydatToString	PhyToString
PhylogeneticInfo	CladisticInfo
PhylogeneticInformation	CladisticInfo
PhyToString	PhyToString
Postorder	Reorder
Postorder.list	Reorder
Postorder.multiPhylo	Reorder
Postorder.numeric	Reorder
Postorder.phylo	Reorder
PostorderEdges	Reorder
Preorder	Reorder
Preorder.list	Reorder
Preorder.multiPhylo	Reorder
Preorder.numeric	Reorder
Preorder.phylo	Reorder
print.TreeNumber	print.TreeNumber
Pruningwise	Reorder
Pruningwise.list	Reorder
Pruningwise.multiPhylo	Reorder
Pruningwise.phylo	Reorder
RandomTree	GenerateTree
ReadAsPhyDat	ReadCharacters
ReadCharacters	ReadCharacters
ReadTntAsPhyDat	ReadCharacters
ReadTntCharacters	ReadCharacters
ReadTntTree	ReadTntTree
Renumber	Renumber
RenumberEdges	Reorder
RenumberTips	RenumberTips
RenumberTips.list	RenumberTips
RenumberTips.multiPhylo	RenumberTips
RenumberTips.phylo	RenumberTips
RenumberTree	Reorder
Reorder	Reorder
replicate64	sapply64
RightmostCharacter	RightmostCharacter
RootedTreeShape	TreeShape
RootedTreeWithShape	TreeShape
RootNode	RootNode
RootNodeDist	Stemwardness
RootNodeDistance	Stemwardness
RootNodeDistance.character	Stemwardness
RootNodeDistance.numeric	Stemwardness
RootOnNode	RootTree
RootTree	RootTree
SampleOne	SampleOne
sapply64	sapply64
SingleTaxonTree	SingleTaxonTree
SisterSize	Stemwardness
SisterSize.character	Stemwardness
SisterSize.numeric	Stemwardness
SortTree	SortTree
SplitFrequency	SplitFrequency
SplitImbalance	TipsInSplits
SplitImbalance.phylo	TipsInSplits
SplitImbalance.Splits	TipsInSplits
SplitInformation	SplitInformation
SplitMatchProbability	SplitMatchProbability
SplitNumber	SplitFrequency
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
Stemwardness	Stemwardness
StringToPhyDat	PhyToString
StringToPhydat	PhyToString
Subsplit	Subsplit
Subtree	Subtree
SupportColor	SupportColour
SupportColour	SupportColour
TCIContext	TotalCopheneticIndex
TCIContext.numeric	TotalCopheneticIndex
TipLabels	TipLabels
TipLabels.character	TipLabels
TipLabels.default	TipLabels
TipLabels.list	TipLabels
TipLabels.matrix	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
TNTText2Tree	ReadTntTree
TntText2Tree	ReadTntTree
TotalCopheneticIndex	TotalCopheneticIndex
TreeIsRooted	TreeIsRooted
TreeNumber	TreeNumber
TreeShape	TreeShape
TreesMatchingSplit	TreesMatchingSplit
TreesMatchingTree	TreesMatchingTree
TreeSplits	SplitFrequency
TreeTools	TreeTools-package
TrivialSplits	TrivialSplits
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
