# Comparison of Phylogenetic Trees Using Quartet and Split Measures

## Documentation for package ‘Quartet’ version 1.1.0

- 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 splits
CompareQuartets | Compare quartet states by explicit enumeration
CompareSplits | Compare status of splits
Distances | Triplet and quartet distances with tqDist
DoNotConflict | Tree Similarity Metrics
ExplicitlyAgree | Tree Similarity Metrics
ManyToManyQuartetAgreement | Status of quartets
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 | Status of quartets
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
TwoListQuartetAgreement | Status of quartets