The identifiability of tree topology for phylogenetic models, including covarion and mixture models.

作者: Elizabeth S. Allman , John A. Rhodes

DOI: 10.1089/CMB.2006.13.1101

关键词: Phylogenetic treeTree rearrangementDiscrete mathematicsPhylogenetic networkIdentifiabilityCovarionMixture modelTheoretical computer scienceTree (data structure)Computational phylogeneticsMathematics

摘要: For a model of molecular evolution to be useful for phylogenetic inference, the topology evolutionary trees must identifiable. That is, from joint distribution predicts, it possible recover tree parameter. We establish identifiability number models, including covarion and variety mixture models with limited classes. The proof is based on introduction more general model, allowing states at internal nodes than leaves, study algebraic formed by distributions which gives rise. Tree first established this through use certain invariants.

参考文章(35)
Kristian Ranestad, Bernd Sturmfels, Nicholas Eriksson, Seth Sullivant, Phylogenetic Algebraic Geometry arXiv: Algebraic Geometry. ,(2004)
Michael D. Hendy, The Relationship Between Simple Evolutionary Tree Models and Observable Sequence Data Systematic Biology. ,vol. 38, pp. 310- 321 ,(1989) , 10.2307/2992397
Elizabeth S. Allman, John A. Rhodes, Phylogenetic invariants for stationary base composition Journal of Symbolic Computation. ,vol. 41, pp. 138- 150 ,(2006) , 10.1016/J.JSC.2005.04.004
Mike Steel, Michael D. Hendy, David Penny, Reconstructing phylogenies from nucleotide pattern probabilities: a survey and some new results Discrete Applied Mathematics. ,vol. 88, pp. 367- 396 ,(1998) , 10.1016/S0166-218X(98)00080-8
L.A. Szekely, M.A. Steel, P.L. Erdos, Fourier Calculus on Evolutionary Trees Advances in Applied Mathematics. ,vol. 14, pp. 200- 216 ,(1993) , 10.1006/AAMA.1993.1011
Bernd Sturmfels, Seth Sullivant, Toric ideals of phylogenetic invariants. Journal of Computational Biology. ,vol. 12, pp. 457- 481 ,(2005) , 10.1089/CMB.2005.12.457