MSCquartets 3.3: Fast Inference of Species Networks and Trees of Blobs under the Multispecies Coalescent

The R package MSCquartets offers a suite of methods for testing and inferring species relationships from gene trees under coalescent models. MSCquartets 3.3 significantly extends the functionality of version 1.0 by implementing the TINNiK and ECToBlob algorithms for inference of the tree of blobs under the network multispecies coalescent model (NMSC). Additionally, it implements the NANUQ+ algorithm, a fast method for inference of level-1 networks. Computational speed of all functionalities is greatly improved through use of C ++ routines, and a Shiny App is introduced for easier exploration of basic analyses. Availability and implementation: MSCquartets 3.3 is available on the Comprehensive R Archive Network, at https://CRAN.R-project.org/package=MSCquartets. The MSCquartets 3.3 Shiny App is available at https://mscquartets.shinyapps.io/MSCq-app/