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MSCquartets
View on CRAN: Click
here
Download and install MSCquartets package within the R console
Install from CRAN:
install.packages("MSCquartets")
Install from Github:
library("remotes")
install_github("cran/MSCquartets") Install by package version:
library("remotes")
install_version("MSCquartets", "3.2") Attach the package and use:
library("MSCquartets")
Maintained by
John Rhodes
[Scholar Profile | Author Map]
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2019-12-16
Latest Update: 2025-03-20
Description:
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) ,
simplex plots of quartet concordance factors as presented by Allman et al. (2020)
, species tree inference methods based on quartet
distances of Rhodes (2019) and Yourdkhani and
Rhodes (2019) , the NANUQ algorithm for inference
of level-1 species networks of Allman et al. (2019) ,
and the TINNIK algorithm for inference of the tree of blobs of an arbitrary
network of Allman et al.(2022) . Software
announcement by Rhodes et al. (2020) .
How to cite:
John Rhodes (2019). MSCquartets: Analyzing Gene Tree Quartets under the Multi-Species Coalescent. R package version 3.2, https://cran.r-project.org/web/packages/MSCquartets. Accessed 05 Aug. 2026.
Previous versions and publish date:
Other packages that cited MSCquartets R package
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Other R packages that MSCquartets depends,
imports, suggests or enhances
Complete documentation for MSCquartets
Functions, R codes and Examples using
the MSCquartets R package
Some associated functions: HolmBonferroni . M0 . MSCquartets-package . NANUQ . NANUQdist . QDC . QDS . T1density . T3density . WQDC . WQDCrecursive . WQDS . WQDSAdjustLengths . dataGeneTreeSample . dataHeliconiusMartin . dataYeastRokas . estimateEdgeLengths . expectedCFs . nexusDist . powerDivStat . pvalHist . quartetDist . quartetNetworkDist . quartetStarTest . quartetStarTestInd . quartetTable . quartetTableCollapse . quartetTableDominant . quartetTableParallel . quartetTablePrint . quartetTableResolved . quartetTestPlot . quartetTreeErrorProb . quartetTreeTest . quartetTreeTestInd . quartetWeightedDist . simplexCoords . simplexLabels . simplexPoint . simplexPrepare . simplexSegment . simplexText . taxonNames .
Some associated R codes: ExpectedCFs.R . MSCquartets.R . NANUQ.R . ParallelTable.R . QuartetTally.R . SimplexPlot.R . StarQuartetHypTest.R . TreeQuartetDist.R . TreeQuartetHypTest.R . WQDCrecursive.R . pHist.R . Full MSCquartets package functions and examples
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