The Identifiability of Tree Topology for Phylogenetic Models, Including Covarion and Mixture Models. - Elizabeth S. Allman; John A. Rhodes (J. Comput. Biol., 2006)

Phylogenetic invariants for stationary base composition. - Elizabeth S. Allman; John A. Rhodes (J. Symb. Comput., 2006)

Phylogenetic ideals and varieties for the general Markov model. - Elizabeth S. Allman; John A. Rhodes (Adv. Appl. Math., 2008)

The Identifiability of Covarion Models in Phylogenetics. - Elizabeth S. Allman; John A. Rhodes (IEEE ACM Trans. Comput. Biol. Bioinform., 2009)

Identifiability of Two-Tree Mixtures for Group-Based Models. - Elizabeth S. Allman; Sonja Petrovic; John A. Rhodes; Seth Sullivant (IEEE ACM Trans. Comput. Biol. Bioinform., 2011)

Species Tree Inference by the STAR Method and Its Generalizations. - Elizabeth S. Allman; James H. Degnan; John A. Rhodes (J. Comput. Biol., 2013)

Tensor Rank, Invariants, Inequalities, and Applications. - Elizabeth S. Allman; Peter D. Jarvis; John A. Rhodes; Jeremy G. Sumner (SIAM J. Matrix Anal. Appl., 2013)

A Semialgebraic Description of the General Markov Model on Phylogenetic Trees. - Elizabeth S. Allman; John A. Rhodes; Amelia Taylor (SIAM J. Discret. Math., 2014)

A Letter from the Guest Editors. - Fred Adler; Elizabeth S. Allman; Lisette G. de Pillis (Am. Math. Mon., 2014)

Statistically Consistent k-mer Methods for Phylogenetic Tree Reconstruction. - Elizabeth S. Allman; John A. Rhodes; Seth Sullivant (J. Comput. Biol., 2017)

Species Tree Inference from Gene Splits by Unrooted STAR Methods. - Elizabeth S. Allman; James H. Degnan; John A. Rhodes (IEEE ACM Trans. Comput. Biol. Bioinform., 2018)

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)

Species Tree Inference from Genomic Sequences Using the Log-Det Distance. - Elizabeth S. Allman; Colby Long; John A. Rhodes (SIAM J. Appl. Algebra Geom., 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)

Parameter Identifiability for a Profile Mixture Model of Protein Evolution. - Samaneh Yourdkhani; Elizabeth S. Allman; John A. Rhodes (J. Comput. Biol., 2021)

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

Parameter Identifiability of a Multitype Pure-Birth Model of Speciation. - Dakota Dragomir; Elizabeth S. Allman; John A. Rhodes (J. Comput. Biol., 2023)

Phylogenomic Models from Tree Symmetries. - Elizabeth S. Allman; Colby Long; John A. Rhodes (SIAM J. Appl. Algebra Geom., 2024)

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)

NANUQ+: A divide-and-conquer approach to network estimation. - Elizabeth S. Allman; Hector Baños; John A. Rhodes; Kristina Wicke (Algorithms Mol. Biol., 2025)