Mathematics and Statistics •
UAF, Fairbanks, AK •
e.allman AT alaska.edu
Papers and Publications
2024
"NANUQ+: A divide-and-conquer approach to network estimation." with H. Banos, J.A. Rhodes, and K. Wicke. bioRxiv"TINNiK: Inference of the Tree of Blobs of a Species Network Under the Coalescent." with H. Banos, J. Mitchell, and J.A. Rhodes, Algorithms for Molecular Biology, 19, (2024). doi
"Identifiability of Level-1 Species Networks from Gene Tree Quartets." with H. Banos, M. Garrote-Lopez, and J. Rhodes, Bull. Math. Biol., Bulletin of Mathematical Biology, 86, 110 (2024), 48 pp. doi
"Anomalous networks under the multispecies coalescent: theory and prevalence." with C. Ane, J. Fogg, H. Banos, and J. Rhodes, J. of Math. Biol., 88 no. 3 (2024), Paper no.29, 36 pp.
"Phylogenomic models from Tree Symmetries." with C. Long and J. Rhodes, SIAM J. on Applied Algebra and Geometry, 8 (1) 114-137. (2024)
2023
"PhyloCoalSimulations: A simulator for network multispecies coalescent models, including a new extension for the inheritance of gene flow." with J. Fogg and C. Ane, Syst. Biol., 72 (5) 1171-1179. (2023). doi"Parameter identifiability of a multitype pure-birth model of speciation." with D. Dragomir and J. Rhodes, J. of Computational Biology, 6 Feb 2023 doi
"Testing Multispecies Coalescent Simulators using Summary Statistics." E.S. Allman, H. Banos-Cervantes and J. Rhodes, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 20 no. 2 (2023) 1613-1618. doi
2022
"A generalized AIC for models with singularities and boundaries." with D. Mitchell and J. Rhodes, submitted."The tree of blobs of a species network: Identifiability under the coalescent." with H. Banos, D. Mitchell, and J. Rhodes, J. of Mathematical Biology, doi.
"Identifiability of species network topologies from genomic sequences using the logDet distance." E.S. Allman, H. Banos, and J. Rhodes, J. Math. Biol., 84 no. 5 (2022) 1–38. doi.
"Gene tree discord, simplex plots, and statistical tests under the coalescent." E.S. Allman, J.D. Mitchell and J. Rhodes, Syst. Biol., 71 no. 4 (2022) 929-942. doi.
2021
"Parameter identifiability for a profile mixture model of protein evolution." S. Yourdkhani, E.S. Allman and J. Rhodes, J. Computational Biology, 28 no. 6 (2021) 570–586. "MSCquartets 1.0: Quartet methods for species trees and networks under the multispecies coalescent model in R." E.S. Allman, H.D. Banos-Cervantes, J.D. Mitchell and J. Rhodes, Bioinformatics, 37 12 (2021) 1766-1768. online
2019
"NANUQ: A method for inferring species networks from gene trees under the coalescent model." E.S. Allman, H. Banos-Cervantes and J.Rhodes, Algorithms for Molecular Biology, 14 no. 24 (2019). doi "Hypothesis testing near singularities and boundaries." E.S. Allman, J. Mitchell and J.Rhodes, Electronic Journal of Statistics, 13 no. 1 (2019) 1250-1293. "Species tree inference from genomic sequences using the log-det distance." Elizabeth S. Allman, Colby Long, and John A. Rhodes, SIAM Journal on Applied Algebra and Geometry, 3 no.1 (2019) 107-127.2018
"Species tree inference from gene splits by Unrooted STAR methods." E. Allman, J. Degnan and J. Rhodes, IEEE/ACM Transactions in Computational Biology and Bioinformatics, 15 no. 1 (2018) 337-342. "Split probabilities and species tree inference under the multispecies coalescent model." E.S. Allman, J.H. Degnan and J.A. Rhodes, Bulletin of Mathematical Biology, 80, no. 1 (2018) 64-103.2017
"Split scores: a tool to quantify phylogenetic signal in genome-scale data." Elizabeth S. Allman, Laura S. Kubatko and John A. Rhodes, Systematic Biology, 66 4 (2017) 620-636.
SplitSup: software for computing splits scores. 2016. Download information on main web page. Current
version 1.02
"Statistically-Consistent k-mer Methods for Phylogenetic Tree Reconstruction."
Elizabeth S. Allman, John A. Rhodes, and Seth Sullivant,
J. of Computational Biology,
24 no. 2 (2017) 153-171.
Available on the arXiv or
here in color. This link includes the supplementary materials too.
2015
"Parameter identifiability of discrete Bayesian networks with hidden variables." Elizabeth S. Allman, John A. Rhodes, Elena Stanghellini, and Marco Valtorta, Journal of Causal Inference, 3 no. 2 (2015) 189-205.
"Tensors of nonnegative rank two."
Elizabeth S. Allman, John A. Rhodes, B. Sturmfels, and P. Zwiernik
Linear Algebra and its Applications,
473 (2015) 37-53.
2014
"A semialgebraic description of the general Markov model on phylogenetic trees." Elizabeth S. Allman, John A. Rhodes, and Amelia Taylor SIAM J. Discrete Math, 28 no. 2 (2014) 736-755.
"A Letter from the Guest Editors," special issue in
Mathematical Biology, E.S. Allman, F.Adler and L. de Pillis,
American Mathematical Monthly, 121 no. 9 (2014) 751-753.
2013
"Tensor Rank, Invariants, Inequalities, and Applications." Elizabeth S. Allman, Peter D. Jarvis, John A. Rhodes, and Jeremy G. Sumner SIAM Journal on Matrix Analysis and Applications, 34 no. 3 (2013) 1014-1045.
"Species tree inference by the STAR method, and generalizations."
Elizabeth S. Allman, James H. Degnan, and John A. Rhodes,
J. Computational Biology, 20 no. 1 (2013) 50-61.
2012
"When Do Phylogenetic Mixture Models Mimic Other Phylogenetic Models?." Elizabeth S. Allman, John A. Rhodes, and Seth Sullivant Systematic Biology, 61 no. 6 (2012) 1049-1059.
2011
"Determining species tree topologies from clade probabilities under the coalescent." Elizabeth S. Allman, James H. Degnan, and John A. Rhodes, Journal of Theoretical Biology, 289 (2011) 96-106.
"Parameter Identifiability in a class of random graph mixture models."
Elizabeth S. Allman, Catherine Matias, and John A. Rhodes,
Journal of Statistical Planning and Inference, 141 no. 5 (2011) 1719-1736.
"Identifying the Rooted Species Tree from the Distribution of Unrooted Gene Trees under the Coalescent." Elizabeth S. Allman, James H. Degnan, and John A. Rhodes, Journal of Mathematical Biology, 62 no.6 (2011) 833-862.
"Identifiability of 2-tree mixtures for group-based models."
Elizabeth S. Allman, Sonja Petrovic, John A. Rhodes, and Seth Sullivant
IEEE/ACM Transactions in Computational Biology and Bioinformatics,
8 no. 3 (2011) 710-722.
Supplementary materials
2010
"Trees, Fast and Accurate." Elizabeth S. Allman and John A. Rhodes, Science, 327 (2010) 1334-1335.
"Estimating trees from filtered data: Identifiability of models for morphological phylogenetics."
Elizabeth S. Allman, Mark T. Holder, and John A. Rhodes,
Journal of Theoretical Biology, 263 (2010) 108-119.
2009
"Identifiability of parameters in latent structure models with many observed variables." Elizabeth S. Allman, Catherine Matias, and John A. Rhodes, Annals of Statistics, 37 no.6A (2009) 3099-3132.
"The identifiability of Covarion models in phylogenetics."
Elizabeth S. Allman and John A. Rhodes,
IEEE/ACM Transactions in Computational Biology and Bioinformatics,
6 no. 1 (2009) 76-88.
2008
"Identifiability of a Markovian model of molecular evolution with gamma-distributed rates." Elizabeth S. Allman, Cecile Ane, and John A. Rhodes, Advances in Applied Probability, 40 no. 1 (2008) 228-249. Former title was "Identifiability of the GTR+Gamma model of molecular evolution."
"The Gaps in the proof of identifiability of the GTR+Gamma+I model."
Elizabeth S. Allman, Cecile Ane, and John A. Rhodes,
This is now included as an appendix to the paper listed above. (June 2007)
"Identifying evolutionary trees and substitution parameters for
the general Markov model with invariable sites ."
Elizabeth S. Allman and John A. Rhodes,
Mathematical Biosciences, 211 no. 1 (2008) 18-33.
Appendix materials: Maple and Singular code.
2007
"Phylogenetic Ideals and Varieties for the General Markov Model." Elizabeth S. Allman and John A. Rhodes, Advances in Applied Mathematics, 40 no. 2 (2008) 127-148. Available (finally) online Jan 10, 2007.
"Molecular Phylogenetics from an Algebraic Viewpoint."
Elizabeth S. Allman and John A. Rhodes,
Statistica Sinica, 17 no. 4 (2007) 1299-1316.
"Phylogenetic Invariants."
Elizabeth S. Allman and John A. Rhodes.
Chapter 4 in Reconstructing Evolution New Mathematical and Computational
Advances,
edited by O. Gascuel and M. Steel (2007).
"Phylogenetics."
Elizabeth S. Allman and John A. Rhodes.
Lecture notes for AMS Short Course "Modeling and
Simulation of Biological Networks."
Chapter 2 in Proceedings of Symposia in
Applied Mathematics,
edited by R. Laubenbacher (2007).
2006
"The identifiability of tree topology for phylogenetic models, including covarion and mixture models." Elizabeth S. Allman and John A. Rhodes, Journal of Computational Biology, 13 no. 5 (2006) 1101-1113.
"Phylogenetic invariants for stationary base composition."
Elizabeth S. Allman and John A. Rhodes,
Journal Symbolic Computation, 41 (2006) 138-150.
2005
"Lecture Notes: The Mathematics of Phylogenetics." Elizabeth S. Allman and John A. Rhodes, Park City Mathematics Institute's summer program in Mathematical Biology, undergraduate program Preprint, June 26, 2005, 1-127.
2004
"Quartets and Parameter Recovery for the General Markov Model
of Sequence Mutation."
Elizabeth S. Allman and John A. Rhodes,
App. Math. Res. Express Vol. 2004, no. 4, 2004, 107-131.
2003
"Phylogenetic Invariants for the General Markov Model of Sequence Mutation." Elizabeth S. Allman and John A. Rhodes, Math. Biosci. 186(2), 2003, 113-144,
2001
"Division algebras with PSL(2,q)-Galois maximal subfields," E.S. Allman and M. Schacher, J. Algebra, 240 no.2 (2001) 808-821.
1999
"Abelian subgroups of finitely generated Kleinian groups are separable." E.S. Allman and E. Hamilton, Bulletin of the London Mathematical Society, 31 no. 2 (1999) 163-172.
1996
Polynomials Without Roots in Division Algebras." Communications in Algebra, 24 no. 13 (1996) 3891-3919.