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>.

Package details

AuthorElizabeth Allman [aut], Hector Banos [aut], Jonathan Mitchell [aut], John Rhodes [aut, cre] (<https://orcid.org/0000-0001-9921-1091>)
MaintainerJohn Rhodes <j.rhodes@alaska.edu>
LicenseMIT + file LICENSE
Version1.1.1
Package repositoryView on CRAN
Installation Install the latest version of this package by entering the following in R:
install.packages("MSCquartets")

Try the MSCquartets package in your browser

Any scripts or data that you put into this service are public.

MSCquartets documentation built on April 19, 2022, 5:08 p.m.