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MSCquartets  

Analyzing Gene Tree Quartets under the Multi-Species Coalescent
View on CRAN: Click here


Download and install MSCquartets package within the R console
Install from CRAN:
install.packages("MSCquartets")

Install from Github:
library("remotes")
install_github("cran/MSCquartets")

Install by package version:
library("remotes")
install_version("MSCquartets", "3.1")



Attach the package and use:
library("MSCquartets")
Maintained by
John Rhodes
[Scholar Profile | Author Map]
First Published: 2019-12-16
Latest Update: 2023-10-27
Description:
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) , simplex plots of quartet concordance factors as presented by Allman et al. (2020) , species tree inference methods based on quartet distances of Rhodes (2019) and Yourdkhani and Rhodes (2019) , the NANUQ algorithm for inference of level-1 species networks of Allman et al. (2019) , and the TINNIK algorithm for inference of the tree of blobs of an arbitrary network of Allman et al.(2022) . Software announcement by Rhodes et al. (2020) .
How to cite:
John Rhodes (2019). MSCquartets: Analyzing Gene Tree Quartets under the Multi-Species Coalescent. R package version 3.1, https://cran.r-project.org/web/packages/MSCquartets. Accessed 07 Apr. 2025.
Previous versions and publish date:
1.0.5 (2019-12-16 12:50), 1.1.0 (2021-01-07 22:00), 1.1.1 (2022-04-19 16:22), 1.1.2 (2022-12-10 11:30), 1.3.1 (2023-06-12 21:10), 1.3.2 (2023-10-28 01:30), 2.0.1 (2024-08-19 01:40), 2.0 (2024-03-23 22:50), 3.0 (2024-10-31 00:30), 3.1 (2025-03-07 20:00)
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Complete documentation for MSCquartets
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