Analyzing Gene Tree Quartets under the Multi-Species Coalescent R package MSCquartets version 3.3 CRAN Task View: Phylogenetics (https://CRAN.R-project.org/view=Phylogenetics) 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>, NANUQ+ routines for resolving multifurcations in the tree of blobs to cycles as in Rhodes et al.(2024) <doi:10.1186/s13015-025-00274-w>, and the ECToBlob algorithm for inference of a network with no anomalous quartets of Allman et al. (2026) (forthcoming). Software announcement by Rhodes et al. (2020) <doi:10.1093/bioinformatics/btaa868>. Software 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 John Rhodes <j.rhodes@alaska.edu> Comprehensive R Archive Network (CRAN) Elizabeth Allman [aut], Hector Banos [aut], Jonathan Mitchell [aut], Kristina Wicke [aut], John Rhodes [aut, cre] (ORCID: <https://orcid.org/0000-0001-9921-1091>) MIT + file LICENSE (https://CRAN.R-project.org/package=MSCquartets/LICENSE) 2026-05-28 application/tgz https://CRAN.R-project.org/package=MSCquartets doi:10.32614/CRAN.package.MSCquartets