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>, and 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>. Software announcement by Rhodes et al. (2020) <doi:10.1093/bioinformatics/btaa868>.

Version:	2.0
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
Published:	2024-03-23
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:	yes
CRAN checks:	MSCquartets results

Documentation:

Reference manual:

MSCquartets.pdf

Downloads:

Package source:	MSCquartets_2.0.tar.gz
Windows binaries:	r-devel: MSCquartets_2.0.zip, r-release: MSCquartets_2.0.zip, r-oldrel: MSCquartets_2.0.zip
macOS binaries:	r-release (arm64): MSCquartets_2.0.tgz, r-oldrel (arm64): MSCquartets_2.0.tgz, r-release (x86_64): MSCquartets_2.0.tgz, r-oldrel (x86_64): MSCquartets_2.0.tgz
Old sources:	MSCquartets archive

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