MSCquartets (version 3.2)
Analyzing Gene Tree Quartets under the Multi-Species Coalescent
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) ,
the TINNIK algorithm for inference of the tree of blobs of an arbitrary
network of Allman et al.(2022) , 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) .