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 |
Maintainer: | John Rhodes <j.rhodes at alaska.edu> |
License: | MIT + file LICENSE |
NeedsCompilation: | no |
CRAN checks: | MSCquartets results |
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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