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 ORCID iD [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_1.1.0.tar.gz
Windows binaries: r-devel: MSCquartets_1.1.0.zip, r-release: MSCquartets_1.1.0.zip, r-oldrel: MSCquartets_1.1.0.zip
macOS binaries: r-release: MSCquartets_1.1.0.tgz, r-oldrel: MSCquartets_1.1.0.tgz
Old sources: MSCquartets archive

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