| 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 |