MSCquartets: Analyzing Gene Tree Quartets under the Multi-Species Coalescent (original) (raw)
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: | 2.0.1 |
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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 |
Suggests: | knitr, rmarkdown |
Published: | 2024-08-18 |
DOI: | 10.32614/CRAN.package.MSCquartets |
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 |
NeedsCompilation: | yes |
CRAN checks: | MSCquartets results |
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