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>, and the NANUQ algorithm for inference of level-1 species networks of Allman et al. (2019) <doi:10.1186/s13015-019-0159-2>. Software announcement by Rhodes et al. (2020) <doi:10.1093/bioinformatics/btaa868>.

Version:	1.1.0
Depends:	R (≥ 3.2.0), ape (≥ 5.0), phangorn
Imports:	RandomFieldsUtils, zipfR, graphics, stats, Rdpack, foreach, doParallel
Published:	2021-01-07
Author:	Elizabeth Allman [aut], Hector Banos [aut], Jonathan Mitchell [aut], John Rhodes [aut, cre]
Maintainer:	John Rhodes <j.rhodes at alaska.edu>
License:	MIT + file LICENSE
NeedsCompilation:	no
CRAN checks:	MSCquartets results

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