Package: Quartet 1.2.6.9001

Martin R. Smith

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:Martin R. Smith [aut, cre, cph], Andreas Sand [ant], Gerth Stølting Brodal [ant], Rolf Fagerberg [ant], Thomas Mailund [ant], Christian N. S. Pedersen [ant], Jens Johansen [ant], Morten K. Holt [ant]

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Bug tracker:https://github.com/ms609/quartet/issues

On CRAN:

bioinformaticscomparisonphylogenetic-treesphylogeneticsquartetquartet-distanceresearch-tooltree

74 exports 9 stars 3.39 score 51 dependencies 15 mentions 27 scripts 442 downloads

Last updated 5 days agofrom:f1faee6fd8. Checks:ERROR: 1 OK: 8. Indexed: no.

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