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>, 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>, and NANUQ+ routines for resolving multifurcations in the tree of blobs to cycles as in Allman et al.(2024) (forthcoming). Software announcement by Rhodes et al. (2020) <doi:10.1093/bioinformatics/btaa868>.
Version: 3.2 Depends: R (≥ 3.5.0), ape (≥ 5.0), phangorn Imports: zipfR, graphics, stats, Rdpack, foreach, doParallel, methods, Rcpp (≥ 1.0.10), igraph (≥ 2.0.0) LinkingTo: Rcpp, RcppProgress Suggests: knitr, rmarkdown Published: 2025-03-20 DOI: 10.32614/CRAN.package.MSCquartets Author: Elizabeth Allman [aut], Hector Banos [aut], Jonathan Mitchell [aut], Kristina Wicke [aut], John Rhodes [aut, cre] Maintainer: John Rhodes <j.rhodes at alaska.edu> License: MIT + file LICENSE NeedsCompilation: yes In views: Phylogenetics CRAN checks: MSCquartets results Documentation: Downloads: Linking:Please use the canonical form https://CRAN.R-project.org/package=MSCquartets to link to this page.
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