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) , 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) , the TINNIK algorithm for inference of the tree of blobs of an arbitrary network of Allman et al.(2022) , NANUQ+ routines for resolving multifurcations in the tree of blobs to cycles as in Rhodes et al.(2024) , and the ECToBlob algorithm for inference of a network with no anomalous quartets of Allman et al. (2026) (forthcoming). Software announcement by Rhodes et al. (2020) .