NANUQ: a method for inferring species networks from gene trees under the coalescent model. - Elizabeth S. Allman; Hector Baños; John A. Rhodes (Algorithms Mol. Biol., 2019)

MSCquartets 1.0: quartet methods for species trees and networks under the multispecies coalescent model in R. - John A. Rhodes; Hector Baños; Jonathan D. Mitchell; Elizabeth S. Allman (Bioinform., 2021)

Testing Multispecies Coalescent Simulators Using Summary Statistics. - Elizabeth S. Allman; Hector Baños; John A. Rhodes (IEEE ACM Trans. Comput. Biol. Bioinform., 2023)

TINNiK: inference of the tree of blobs of a species network under the coalescent model. - Elizabeth S. Allman; Hector Baños; Jonathan D. Mitchell; John A. Rhodes (Algorithms Mol. Biol., 2024)

Identifying circular orders for blobs in phylogenetic networks. - John A. Rhodes; Hector Baños; Jingcheng Xu; Cécile Ané (Adv. Appl. Math., 2025)