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>, the species tree inference routines based on quartet distances of Rhodes (2019) <doi:10.1109/TCBB.2019.2917204> and Yourdkhani and Rhodes (2019), and the NANUQ algorithm for inference of level-1 species networks of Allman et al. (2019) <arXiv:1905.07050>.

Version: 1.0.5
Depends: R (≥ 3.2.0), ape (≥ 5.0), phangorn
Imports: RandomFieldsUtils, zipfR, graphics, stats, Rdpack
Published: 2019-12-16
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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Reference manual: MSCquartets.pdf
Package source: MSCquartets_1.0.5.tar.gz
Windows binaries: r-devel: MSCquartets_1.0.5.zip, r-devel-gcc8: MSCquartets_1.0.5.zip, r-release: MSCquartets_1.0.5.zip, r-oldrel: MSCquartets_1.0.5.zip
OS X binaries: r-release: MSCquartets_1.0.5.tgz, r-oldrel: MSCquartets_1.0.5.tgz

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