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: |
2.0.1 |
| 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 LICENSE |
| NeedsCompilation: |
yes |
| CRAN checks: |
MSCquartets results |
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