Comparison of Phylogenetic Trees Using Quartet and Bipartition Measures


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Documentation for package ‘Quartet’ version 1.0.2

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AllPairsQuartetAgreement Triplet and quartet distances with tqDist
AllPairsQuartetDistance Triplet and quartet distances with tqDist
AllPairsTripletDistance Triplet and quartet distances with tqDist
AllQuartets List all quartets
BipartitionPoints Plot tree differences on ternary plots
BipartitionStatus Matching partitions
CompareBipartitions Compare status of bipartitions
CompareQuartets Compare quartet states by explicit enumeration
CompareSplits Compare status of bipartitions
Distances Triplet and quartet distances with tqDist
DoNotConflict Tree similarity metrics
ExplicitlyAgree Tree similarity metrics
ManyToManyQuartetAgreement tqDist wrapper
MarczewskiSteinhaus Tree similarity metrics
OneToManyQuartetAgreement Triplet and quartet distances with tqDist
PairsQuartetDistance Triplet and quartet distances with tqDist
PairsTripletDistance Triplet and quartet distances with tqDist
PlotQuartet Plot quartet on a tree topology
QuartetAgreement Triplet and quartet distances with tqDist
QuartetDistance Triplet and quartet distances with tqDist
QuartetDivergence Tree similarity metrics
QuartetPoints Plot tree differences on ternary plots
QuartetState Quartet State(s)
QuartetStates Quartet State(s)
QuartetStatus Status of quartets
ResolvedQuartets Count resolved quartets
ResolvedTriplets Count resolved quartets
RobinsonFoulds Tree similarity metrics
SemiStrictJointAssertions Tree similarity metrics
SharedBipartitionStatus Matching partitions
SharedQuartetStatus Status of quartets
SharedSplitStatus Matching partitions
SimilarityMetrics Tree similarity metrics
SingleTreeQuartetAgreement tqDist wrapper
SplitPoints Plot tree differences on ternary plots
SplitStatus Matching partitions
sq_trees Eighteen trees
SteelPenny Tree similarity metrics
StrictJointAssertions Tree similarity metrics
SymmetricDifference Tree similarity metrics
SymmetricDifferenceLineEnds Plot contours of equal symmetric difference on a ternary plot
SymmetricDifferenceLines Plot contours of equal symmetric difference on a ternary plot
TQAE tqDist wrapper
TQDist tqDist wrapper
TripletDistance Triplet and quartet distances with tqDist