Package: MSCquartets 2.0.1

MSCquartets: Analyzing Gene Tree Quartets under the Multi-Species Coalescent

Methods for analyzing and using quartets displayed on a collection of gene trees, primarily to make inferences about the species tree or network under the multi-species coalescent model. These include quartet hypothesis tests for the model, as developed by Mitchell et al. (2019) <doi:10.1214/19-EJS1576>, simplex plots of quartet concordance factors as presented by Allman et al. (2020) <doi:10.1101/2020.02.13.948083>, species tree inference methods based on quartet distances of Rhodes (2019) <doi:10.1109/TCBB.2019.2917204> and Yourdkhani and Rhodes (2019) <doi:10.1007/s11538-020-00773-4>, the NANUQ algorithm for inference of level-1 species networks of Allman et al. (2019) <doi:10.1186/s13015-019-0159-2>, and the TINNIK algorithm for inference of the tree of blobs of an arbitrary network of Allman et al.(2022) <doi:10.1007/s00285-022-01838-9>. Software announcement by Rhodes et al. (2020) <doi:10.1093/bioinformatics/btaa868>.

Authors:Elizabeth Allman [aut], Hector Banos [aut], Jonathan Mitchell [aut], John Rhodes [aut, cre]

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56 exports 0.36 score 27 dependencies 7 scripts 564 downloads

Last updated 30 days agofrom:fdec5389c5. Checks:OK: 9. Indexed: yes.

Exports:BQinferencecollapseEdgescompatibleSplitscutDensityestimateEdgeLengthsexpectedCFsHolmBonferroniinitBquartetsM0NANUQNANUQdistnexusDistnodeGroupspowerDivStatpvalHistQDCQDSquartetBTinferencePlotquartetCutMLEquartetCutTestquartetCutTestIndquartetDistquartetNetworkDistquartetStarTestquartetStarTestIndquartetTablequartetTableCollapsequartetTableDominantquartetTableParallelquartetTablePrintquartetTableResolvedquartetTallyCppquartetTestPlotquartetTreeErrorProbquartetTreeTestquartetTreeTestIndquartetWeightedDistsimplexCoordssimplexLabelssimplexPointsimplexPreparesimplexSegmentsimplexTextsortQuartetTableRowsT1densityT3densitytaxonNamesTINNIKTINNIKdisttopDisttreeFromSplitstreeOfBlobsWQDCWQDCrecursiveWQDSWQDSAdjustLengths

Dependencies:apeclicodetoolscpp11digestdoParallelfastmatchforeachgenericsglueigraphiteratorslatticelifecyclemagrittrMatrixnlmephangornpkgconfigquadprogrbibutilsRcppRcppProgressRdpackrlangvctrszipfR