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>, 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: |
1.1.1 |
| Depends: |
R (≥ 3.2.0), ape (≥ 5.0), phangorn |
| Imports: |
RandomFieldsUtils, zipfR, graphics, stats, Rdpack, foreach, doParallel, methods |
| Published: |
2022-04-19 |
| 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: |
no |
| CRAN checks: |
MSCquartets results |
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