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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>, 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 + fileLICENSE
NeedsCompilation:	yes
In views:	Phylogenetics
CRAN checks:	MSCquartets results

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