MSCquartets 1.0: quartet methods for species trees and networks under the multispecies coalescent model in R.

Abstract

MSCquartets is an R package for species tree hypothesis testing, inference of species trees and inference of species networks under the Multispecies Coalescent model of incomplete lineage sorting and its network analog. Input for these analyses are collections of metric or topological locus trees which are then summarized by the quartets displayed on them. Results of hypothesis tests at user-supplied levels are displayed in a simplex plot by color-coded points. The package implements the QDC and WQDC algorithms for topological and metric species tree inference, and the NANUQ algorithm for level-1 topological species network inference, all of which give statistically consistent estimators under the model. MSCquartets is available through the Comprehensive R Archive Network: https://CRAN.R-project.org/package=MSCquartets.