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>, 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>, and NANUQ+ routines for resolving multifurcations in the tree of blobs to cycles as in Allman et al.(2024) (forthcoming). Software announcement by Rhodes et al. (2020) <doi:10.1093/bioinformatics/btaa868>.
| Version: | 3.0 |
| 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 |
| Suggests: | knitr, rmarkdown |
| Published: | 2024-10-30 |
| DOI: | 10.32614/CRAN.package.MSCquartets |
| Author: | Elizabeth Allman [aut],
Hector Banos [aut],
Jonathan Mitchell [aut],
Kristina Wicke [aut],
John Rhodes  [aut,
cre] |
| Maintainer: | John Rhodes <j.rhodes at alaska.edu> |
| License: | MIT + file LICENSE |
| NeedsCompilation: | yes |
| In views: | Phylogenetics |
| CRAN checks: | MSCquartets results |
Documentation:
| Reference manual: | MSCquartets.pdf |
| Vignettes: |
Inferring a Level-1 network with the NANUQplus routine (source, R code) Inferring a Tree of Blobs with TINNIK (source, R code) |
Downloads:
| Package source: | MSCquartets_3.0.tar.gz |
| Windows binaries: | r-devel: MSCquartets_3.0.zip, r-release: MSCquartets_3.0.zip, r-oldrel: MSCquartets_3.0.zip |
| macOS binaries: | r-release (arm64): MSCquartets_3.0.tgz, r-oldrel (arm64): MSCquartets_3.0.tgz, r-release (x86_64): MSCquartets_3.0.tgz, r-oldrel (x86_64): MSCquartets_3.0.tgz |
| Old sources: | MSCquartets archive |
Linking:
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