Relevant phylogenetic invariants of evolutionary models

Journal de Mathématiques Pures et Appliquées - Tập 96 - Trang 207-229 - 2011
Marta Casanellas1, Jesús Fernández-Sánchez1
1Dpt. Matemàtica Aplicada I, ETSEIB-UPC, Avinguda Diagonal 647, 08028 Barcelona, Spain

Tài liệu tham khảo

Allman, 2003, Phylogenetic invariants for the general Markov model of sequence mutation, Math. Biosci., 186, 113, 10.1016/j.mbs.2003.08.004 Allman, 2006, The identifiability of tree topology for phylogenetic models, including covarion and mixture models, J. Comput. Biol., 13, 1101, 10.1089/cmb.2006.13.1101 Allman, 2007, Phylogenetic ideals and varieties for the general Markov model, Adv. in Appl. Math., 40, 127, 10.1016/j.aam.2006.10.002 Allman, 2008, Identifying evolutionary trees and substitution parameters for the general Markov model with invariable sites, Math. Biosci., 211, 18, 10.1016/j.mbs.2007.09.001 Barry, 1987, Asynchronous distance between homologous DNA sequences, Biometrics, 43, 261, 10.2307/2531811 Buneman, 1971, The recovery of trees from measures of dissimilarity, 387 Casanellas, 2007, Performance of a new invariants method on homogeneous and nonhomogeneous quartet trees, Mol. Biol. Evol., 24, 288, 10.1093/molbev/msl153 Casanellas, 2008, Geometry of the Kimura 3-parameter model, Adv. in Appl. Math., 41, 265, 10.1016/j.aam.2007.09.003 Casanellas, 2005, Catalog of small trees Casanellas, 2005, The strand symmetric model Cavender, 1987, Invariants of phylogenies in a simple case with discrete states, J. Classification, 4, 57, 10.1007/BF01890075 Draisma, 2009, On the ideals of equivariants tree models, Math. Ann., 344, 619, 10.1007/s00208-008-0320-6 Eriksson, 2005, Tree construction using singular value decomposition, 347 Felsenstein, 1991, Counting phylogenetic invariants in some simple cases, J. Theoret. Biol., 152, 357, 10.1016/S0022-5193(05)80200-0 Fulton, 1991, Representation Theory, vol. 129 L. Garcia-Puente, Algebraic statistics in model selection, in: M. Chickering, J. Halpern (Eds.), Proceedings of the 20th Conference on Uncertainty in Artificial Intelligence, 2004, pp. 177–184. T. Jukes, C. Cantor, Evolution of protein molecules, in: Mammalian Protein Metabolism, 1969, pp. 21–132. Kimura, 1980, A simple method for estimating evolutionary rates of base substitution through comparative studies of nucleotide sequences, J. Mol. Evol., 16, 111, 10.1007/BF01731581 Kimura, 1981, Estimation of evolutionary sequences between homologous nucleotide sequences, Proc. Natl. Acad. Sci. USA, 78, 454, 10.1073/pnas.78.1.454 Lake, 1987, A rate-independent technique for analysis of nucleic acid sequences: evolutionary parsimony, Mol. Biol. Evol., 4, 167 2005 Serre, 1977 Steel, 1994, Recovering a tree from the leaf colourations it generates under a Markov model, Appl. Math. Lett., 7, 19, 10.1016/0893-9659(94)90024-8 Steel, 1992, Spectral analysis and a closest tree method for genetic sequences, Appl. Math. Lett., 5, 63, 10.1016/0893-9659(92)90016-3 Sturmfels, 2005, Toric ideals of phylogenetic invariants, J. Comput. Biol., 12, 204, 10.1089/cmb.2005.12.204