# Comparison of Phylogenetic Trees Using Quartet and Split Measures

## Documentation for package ‘Quartet’ version 1.3.0

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

## Help Pages

AllPairsQuartetAgreement | Direct entry points to "tqDist" functions
AllPairsQuartetDistance | Direct entry points to "tqDist" functions
AllPairsTripletDistance | Direct entry points to "tqDist" functions
AllQuartets | List all quartets
AllQuartets.numeric | List all quartets
AllQuartets.phylo | 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
CompareQuartetsMulti | Compare one tree's quartets against others'
CompareSplits | Compare status of splits
Distances | Direct entry points to "tqDist" functions
DoNotConflict | Tree similarity measures
ExplicitlyAgree | Tree similarity measures
ManyToManyQuartetAgreement | Status of quartets
MarczewskiSteinhaus | Tree similarity measures
OneToManyQuartetAgreement | Direct entry points to "tqDist" functions
PairsQuartetDistance | Direct entry points to "tqDist" functions
PairsTripletDistance | Direct entry points to "tqDist" functions
PlotQuartet | Plot quartet on tree topologies
QuartetAgreement | Direct entry points to "tqDist" functions
QuartetDistance | Direct entry points to "tqDist" functions
QuartetDivergence | Tree similarity measures
QuartetPoints | Plot tree differences on ternary plots
QuartetState | Quartet State(s)
QuartetStates | Quartet State(s)
QuartetStates.list | Quartet State(s)
QuartetStates.multiPhylo | Quartet State(s)
QuartetStates.Splits | Quartet State(s)
QuartetStatus | Status of quartets
RawSymmetricDifference | Tree similarity measures
ResolvedQuartets | Count resolved quartets
ResolvedTriplets | Count resolved quartets
RobinsonFoulds | Tree similarity measures
SemiStrictJointAssertions | Tree similarity measures
SharedBipartitionStatus | Matching partitions
SharedQuartetStatus | Status of quartets
SharedSplitStatus | Matching partitions
SimilarityMetrics | Tree similarity measures
SimilarityToReference | Tree similarity measures
SingleTreeQuartetAgreement | Status of quartets
SplitPoints | Plot tree differences on ternary plots
SplitStatus | Matching partitions
sq_trees | Eighteen example trees
SteelPenny | Tree similarity measures
StrictJointAssertions | Tree similarity measures
SymmetricDifference | Tree similarity measures
SymmetricDifferenceLineEnds | Plot contours of equal symmetric difference on a ternary plot
SymmetricDifferenceLines | Plot contours of equal symmetric difference on a ternary plot
TQAE | Wrapper for tqDist
TQDist | Wrapper for tqDist
TripletDistance | Direct entry points to "tqDist" functions
TwoListQuartetAgreement | Status of quartets
VisualizeQuartets | Visualize quartet difference on trees, by split