# Comparison of Phylogenetic Trees Using Quartet and Bipartition Measures

## Documentation for package ‘Quartet’ version 1.0.2

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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