MSCquartets

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.

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