Package: Quartet 1.2.7
Quartet: Comparison of Phylogenetic Trees Using Quartet and Split Measures
Calculates the number of four-taxon subtrees consistent with a pair of cladograms, calculating the symmetric quartet distance of Bandelt & Dress (1986), Reconstructing the shape of a tree from observed dissimilarity data, Advances in Applied Mathematics, 7, 309-343 <doi:10.1016/0196-8858(86)90038-2>, and using the tqDist algorithm of Sand et al. (2014), tqDist: a library for computing the quartet and triplet distances between binary or general trees, Bioinformatics, 30, 2079–2080 <doi:10.1093/bioinformatics/btu157> for pairs of binary trees.
Authors:
Quartet_1.2.7.tar.gz
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Quartet.pdf |Quartet.html✨
Quartet/json (API)
NEWS
# Install 'Quartet' in R: |
install.packages('Quartet', repos = c('https://ms609.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/ms609/quartet/issues
- sq_trees - Eighteen example trees
bioinformaticscomparisonphylogenetic-treesphylogeneticsquartetquartet-distanceresearch-tooltree
Last updated 6 days agofrom:00ff0891fb. Checks:OK: 9. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Nov 03 2024 |
R-4.5-win-x86_64 | OK | Nov 03 2024 |
R-4.5-linux-x86_64 | OK | Nov 03 2024 |
R-4.4-win-x86_64 | OK | Nov 03 2024 |
R-4.4-mac-x86_64 | OK | Nov 03 2024 |
R-4.4-mac-aarch64 | OK | Nov 03 2024 |
R-4.3-win-x86_64 | OK | Nov 03 2024 |
R-4.3-mac-x86_64 | OK | Nov 03 2024 |
R-4.3-mac-aarch64 | OK | Nov 03 2024 |
Exports:.AddSlice.CheckSize.NormalizeStatus.StatusToArray.StatusToMatrixAllPairsQuartetAgreementAllPairsQuartetDistanceAllPairsTripletDistanceAllQuartetsBipartitionPointsBipartitionStatusCompareBipartitionsCompareQuartetsCompareQuartetsMultiCompareSplitsDoNotConflictExplicitlyAgreeManyToManyQuartetAgreementMarczewskiSteinhausOneToManyQuartetAgreementPairSharedQuartetStatusPairSharedSplitStatusPairsQuartetDistancePairsTripletDistancePlotQuartetQuartetAgreementQuartetDistanceQuartetDivergenceQuartetPointsQuartetStateQuartetStatesQuartetStatusRawSymmetricDifferenceResolvedQuartetsResolvedTripletsRobinsonFouldsSemiStrictJointAssertionsSharedBipartitionStatusSharedQuartetStatusSharedSplitStatusSimilarityMetricsSimilarityToReferenceSingleTreeQuartetAgreementSplitPointsSplitStatusSteelPennyStrictJointAssertionsSymmetricDifferenceSymmetricDifferenceLineEndsSymmetricDifferenceLinesTQAETQDisttqdist_AllPairsQuartetAgreementtqdist_AllPairsQuartetAgreementChartqdist_AllPairsQuartetAgreementEdgetqdist_AllPairsQuartetDistancetqdist_AllPairsQuartetDistanceChartqdist_AllPairsQuartetDistanceEdgetqdist_AllPairsTripletDistancetqdist_OneToManyQuartetAgreementtqdist_OneToManyQuartetAgreementChartqdist_OneToManyQuartetAgreementEdgetqdist_PairsQuartetDistancetqdist_PairsTripletDistancetqdist_QuartetAgreementtqdist_QuartetAgreementChartqdist_QuartetAgreementEdgetqdist_QuartetDistancetqdist_TripletDistanceTQFileTripletDistanceTwoListQuartetAgreementValidateQuartetFileVisualizeQuartets
Dependencies:apebase64encbitbit64bitopsbslibcachemclicolorspacecommonmarkcrayondigestfastmapfastmatchfontawesomefsgluehtmltoolshttpuvjquerylibjsonlitelaterlatticelifecyclemagrittrmemoisemimenlmePlotToolspromisesR.cacheR.methodsS3R.ooR.utilsR6rappdirsrbibutilsRcppRcppHungarianRCurlRdpackrlangsassshinysourcetoolsspTernaryTreeToolsviridisLitewithrxtable
Readme and manuals
Help Manual
Help page | Topics |
---|---|
List all quartets | AllQuartets AllQuartets.numeric AllQuartets.phylo |
Compare quartet states by explicit enumeration | CompareQuartets |
Compare one tree's quartets against others' | CompareQuartetsMulti |
Compare status of splits | CompareBipartitions CompareSplits |
Direct entry points to "tqDist" functions | AllPairsQuartetAgreement AllPairsQuartetDistance AllPairsTripletDistance Distances OneToManyQuartetAgreement PairsQuartetDistance PairsTripletDistance QuartetAgreement QuartetDistance TripletDistance |
Plot quartet on tree topologies | PlotQuartet |
Plot tree differences on ternary plots | BipartitionPoints QuartetPoints SplitPoints |
Quartet State(s) | QuartetState QuartetStates QuartetStates.list QuartetStates.multiPhylo QuartetStates.Splits |
Count resolved quartets | ResolvedQuartets ResolvedTriplets |
Status of quartets | ManyToManyQuartetAgreement QuartetStatus SharedQuartetStatus SingleTreeQuartetAgreement TwoListQuartetAgreement |
Tree similarity measures | DoNotConflict ExplicitlyAgree MarczewskiSteinhaus QuartetDivergence RawSymmetricDifference RobinsonFoulds SemiStrictJointAssertions SimilarityMetrics SimilarityToReference SteelPenny StrictJointAssertions SymmetricDifference |
Matching partitions | BipartitionStatus SharedBipartitionStatus SharedSplitStatus SplitStatus |
Eighteen example trees | sq_trees |
Plot contours of equal symmetric difference on a ternary plot | SymmetricDifferenceLineEnds SymmetricDifferenceLines |
Wrapper for tqDist | TQAE TQDist |
Visualize quartet difference on trees, by split | VisualizeQuartets |