Package: Quartet 1.2.7

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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Quartet.pdf |Quartet.html✨
Quartet/json (API)
NEWS

# Install 'Quartet' in R:
install.packages('Quartet', repos = c('https://phylotastic.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

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

Pkgdown site:https://ms609.github.io

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:

On CRAN:

bioinformaticscomparisonphylogenetic-treesphylogeneticsquartetquartet-distanceresearch-tooltreecpp

8.02 score 13 stars 40 scripts 722 downloads 15 mentions 74 exports 51 dependencies

Last updated 14 days agofrom:5e8ad9d3df. Checks:9 OK. Indexed: no.

TargetResultLatest binary
Doc / VignettesOKJan 16 2025
R-4.5-win-x86_64OKJan 16 2025
R-4.5-linux-x86_64OKJan 16 2025
R-4.4-win-x86_64OKJan 16 2025
R-4.4-mac-x86_64OKJan 16 2025
R-4.4-mac-aarch64OKJan 16 2025
R-4.3-win-x86_64OKJan 16 2025
R-4.3-mac-x86_64OKJan 16 2025
R-4.3-mac-aarch64OKJan 16 2025

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

About the quartet distance

Martin R. Smith

Rendered fromQuartet-Distance.Rmdusingknitr::rmarkdownon Jan 16 2025.

Last update: 2024-10-31
Started: 2020-03-25

Getting started with Quartet

Martin R. Smith

Rendered fromUsing-Quartet.Rmdusingknitr::rmarkdownon Jan 16 2025.

Last update: 2025-01-16
Started: 2020-03-25

Readme and manuals

Help Manual

Help pageTopics
List all quartetsAllQuartets AllQuartets.numeric AllQuartets.phylo
Compare quartet states by explicit enumerationCompareQuartets
Compare one tree's quartets against others'CompareQuartetsMulti
Compare status of splitsCompareBipartitions CompareSplits
Direct entry points to "tqDist" functionsAllPairsQuartetAgreement AllPairsQuartetDistance AllPairsTripletDistance Distances OneToManyQuartetAgreement PairsQuartetDistance PairsTripletDistance QuartetAgreement QuartetDistance TripletDistance
Plot quartet on tree topologiesPlotQuartet
Plot tree differences on ternary plotsBipartitionPoints QuartetPoints SplitPoints
Quartet State(s)QuartetState QuartetStates QuartetStates.list QuartetStates.multiPhylo QuartetStates.Splits
Count resolved quartetsResolvedQuartets ResolvedTriplets
Status of quartetsManyToManyQuartetAgreement QuartetStatus SharedQuartetStatus SingleTreeQuartetAgreement TwoListQuartetAgreement
Tree similarity measuresDoNotConflict ExplicitlyAgree MarczewskiSteinhaus QuartetDivergence RawSymmetricDifference RobinsonFoulds SemiStrictJointAssertions SimilarityMetrics SimilarityToReference SteelPenny StrictJointAssertions SymmetricDifference
Matching partitionsBipartitionStatus SharedBipartitionStatus SharedSplitStatus SplitStatus
Eighteen example treessq_trees
Plot contours of equal symmetric difference on a ternary plotSymmetricDifferenceLineEnds SymmetricDifferenceLines
Wrapper for tqDistTQAE TQDist
Visualize quartet difference on trees, by splitVisualizeQuartets