Invertibility of the TKF model of sequence evolution

Mathematical Biosciences

Volumn 200, Issue 1, 2006, Pages 58-75

  Thatte, Bhalchandra D ^a  

^a MASSEY UNIVERSITY   (New Zealand)

Author keywords

Alignment; DNA sequence evolution models; Identifiability; Phylogenetics

Indexed keywords

DNA; DNA SEQUENCES; MATHEMATICAL MODELS; PROBABILITY;

DNA SEQUENCE EVOLUTION MODELS; IDENTIFIABILITY; PHYLOGENETICS;

TREES (MATHEMATICS);

EVOLUTION;

ARTICLE; DNA SEQUENCE; MATHEMATICAL MODEL; PHYLOGENETIC TREE; PROBABILITY; STRUCTURAL HOMOLOGY;

ALGORITHMS; EVOLUTION, MOLECULAR; MODELS, GENETIC; PHYLOGENY; SEQUENCE ALIGNMENT;

EID: 33644555241     PISSN: 00255564     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.mbs.2005.12.025     Document Type: Article

References (18)

1. J. Felsenstein Evolutionary trees from DNA sequences: a maximum likelihood approach J. Mol. Evol. 17 1981 368
2. J.T. Chang, and J.A. Hartigan Reconstruction of evolutionary trees from pairwise distributions on current species E.M. Keramidas Computing Science and Statistics: Proceedings of the 23rd Symposium on the Interface 1991 Interface Foundation Fairfax Station, VA 254
3. M. Steel, M. Hendy, and D. Penny Reconstructing phylogenies from nucleotide probabilities - a survey and some new results Discrete Appl. Math. 88 1998 367
4. S.L. Hakimi, and A.N. Patrinos The distance matrix of a graph and its tree realization Quart. Appl. Math. 30 1972 255
5. K.A. Zaretskii Constructing trees from the set of distances between pendant vertices Usp. Mat. Nauk. 20 1965 90
6. P. Buneman The recovery of trees from measures of dissimilarity F.R. Hodson D.G. Kendall P. Tautu Mathematics in the Archaeological and Historical Sciences 1971 Edinburgh University Edinburgh 387
7. M. Hendy The relationship between simple evolutionary tree models and observable sequence data Syst. Zool. 38 1989 310
8. M. Hendy, and D. Penny A framework for the quantitative study of evolutionary trees Syst. Zool. 38 1989 297
9. M. Hendy, and D. Penny Spectral analysis of phylogenetic data J. Classif. 10 1993 5
10. J. Chang Full reconstruction of Markov models on evolutionary trees: identifiability and consistency Math. Biosci. 137 1996 51
11. J. Thorne, H. Kishino, and J. Felsenstein An evolutionary model for maximum likelihood alignment of DNA sequences J. Mol. Evol. 33 1991 114
12. J. Thorne, H. Kishino, and J. Felsenstein Inching toward reality: an improved likelihood model of sequence evolution J. Mol. Evol. 34 1992 3
13. M. Steel, and J. Hein Applying the Thorne-Kishino-Felsenstein model to sequence evolution on a star-shaped tree Appl. Math. Lett. 14 2001 679
14. G. Lunter, I. Miklos, A. Drummond, J.L. Jensen, and J. Hein Bayesian phylogenetic inference under a statistical insertion-deletion model Lect. Notes Bioinformatics 2812 2003 228
15. J. Hein, J.L. Jensen, and C.N.S. Pedersen Recursions for statistical multiple alignment Proc. Natl. Acad. Sci. USA 100 25 2003 14960
16. I. Miklos, G. Lunter, and I. Holmes A 'Long Indel' model for evolutionary sequence alignment Mol. Biol. Evol. 10 3 2004 529
17. P. Erdös, M. Steel, L. Székely, and T. Warnow A few logs suffice to build (almost) all trees (I) Random Struct. Algor. 14 2 1999 153
18. D. Metzler, R. Fleißner, A. Wakolbinger, and A. von Haeseler Stochastic insertion-deletion processes and statistical sequence alignment A. Greven D. Deuschel Interacting Stochastic Systems 2005 Springer Heidelberg/Berlin 247