Recent Papers and Publications
"Identifiability of 2-tree mixtures for group-based models"
Elizabeth S. Allman, Sonja Petrovic, John A. Rhodes, and Seth Sullivant
Preprint on the arXiv, September 2009
Supplementary materials
"Estimating trees from filtered data: Identifiability of models for morphological phylogenetics"
Elizabeth S. Allman, Mark T. Holder, and John A. Rhodes
Preprint on the arXiv, May 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.
Preprint on the arXiv, September 2008
"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.
"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.
Preprint or on the arXiv, February 24, 2007, 1-19.
Appendix materials: Maple and Singular code.
"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.
Preprint, October 20, 2004
http://arxiv.org/abs/math.AG/0410604 or GM2plus.pdf
"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).
"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.
Preprint, November 9, 2005, 1-30. covarion.pdf or on the arXiv
Other papers are available here.