| 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 |