On the variational distance of two trees
M. A. Steel and L. A. Székely
Source: Ann. Appl. Probab. Volume 16, Number 3
(2006), 1563-1575.
Abstract
A widely studied model for generating sequences is to “evolve” them on a tree according to a symmetric Markov process. We prove that model trees tend to be maximally “far apart” in terms of variational distance.
First Page:
Show
Hide
Keywords: Cavender–Farris–Neyman model; symmetric binary channel; tree-based Markov process; Yule–Harding distribution; phylogeny reconstruction; sequence evolution; q-state Potts model; Jukes–Cantor model; variational distance
Full-text: Open access
Links and Identifiers
Permanent link to this document: http://projecteuclid.org/euclid.aoap/1159804991
Digital Object Identifier: doi:10.1214/105051606000000196
Zentralblatt MATH identifier: 1111.62111
Mathematical Reviews number (MathSciNet): MR2260073
References
Alon, N. and Spencer, J. H. (1992). The Probabilistic Method. Wiley, New York.
Mathematical Reviews (MathSciNet): MR1140703
Zentralblatt MATH: 0767.05001
Ambainis, A., Desper, R., Farach, M. and Kannan, S. (1997). Nearly tight bounds on the learnability of evolution. In Proc. 38th Annual Symposium on Foundations of Computer Science 524--533. IEEE Computer Society, Piscataway, NJ.
Bininda-Emonds, O. R. P., Brady, S. G., Kim, J. and Sanderson, M. J. (2001). Scaling of accuracy in extremely large phylogenetic trees. Pacific Symposium on Biocomputing 6 547--558.
Bollobás, B. (2001). Random Graphs, 2nd ed. Cambridge Univ. Press.
Mathematical Reviews (MathSciNet): MR1864966
Daskalakis, C., Mossel, E. and Roch, S. (2006). Optimal phylogenetic reconstruction. In Proceedings of the Thirty-Eight Annual ACM Symposium on Theory of Computing 159--168. ACM, New York.
Mathematical Reviews (MathSciNet): MR2277141
Digital Object Identifier: doi:10.1145/1132516.1132540
Erdős, P. L., Steel, M. A., Székely, L. A. and Warnow, T. J. (1999). A few logs suffice to build (almost) all trees. I. Random Structures Algorithms 14 153--184.
Mathematical Reviews (MathSciNet): MR1667319
Erdös, P. L., Steel, M.A., Székely, L. A. and Warnow, T. (1999). A few logs suffice to build (almost) all trees. II. Theor. Comput. Sci. 221 77--118.
Mathematical Reviews (MathSciNet): MR1700821
Digital Object Identifier: doi:10.1016/S0304-3975(99)00028-6
Zentralblatt MATH: 0933.68100
Evans, W., Kenyon, C., Peres, Y. and Schulman, L. J. (2000). Broadcasting on trees and the Ising model. Adv. in Appl. Probab. 10 410--433.
Mathematical Reviews (MathSciNet): MR1768240
Digital Object Identifier: doi:10.1214/aoap/1019487349
Project Euclid: euclid.aoap/1019487349
Zentralblatt MATH: 1052.60076
Farach, M. and Kannan, S. (1996). Efficient algorithms for inverting evolution. In Proceedings of the Twenty-Eight Annual ACM Symposium on Theory of Computing 230--236. ACM, New York.
Mathematical Reviews (MathSciNet): MR1427518
Zentralblatt MATH: 0911.92020
Digital Object Identifier: doi:10.1145/237814.237868
Farach, M. and Kannan, S. (1999). Efficient algorithms for inverting evolution. J. ACM 46 437--449.
Mathematical Reviews (MathSciNet): MR1812126
Digital Object Identifier: doi:10.1145/320211.320212
Zentralblatt MATH: 1065.68662
Fu, Y.-X. and Li, W.-H. (1991). Necessary and sufficient conditions for the existence of certain quadratic invariants under a phylogenetic tree. Math. Biosci. 105 229--238.
Mossel, E. (2004). Phase transitions in Phylogeny Mossel, E. Trans. Amer. Math. Soc. 356 2379--2404.
Mathematical Reviews (MathSciNet): MR2048522
Digital Object Identifier: doi:10.1090/S0002-9947-03-03382-8
Zentralblatt MATH: 1041.92018
Mossel, E. and Peres, Y. (2003). Information flow on trees. Ann. Appl. Probab. 13 817--844.
Mathematical Reviews (MathSciNet): MR1994038
Digital Object Identifier: doi:10.1214/aoap/1060202828
Project Euclid: euclid.aoap/1060202828
Zentralblatt MATH: 1050.60082
Rice, K. and Warnow, T. (1997). Parsimony is hard to beat. Computing and Combinatorics. Lecture Notes in Comput. Sci. 1276 124--133. Springer, Berlin.
Mathematical Reviews (MathSciNet): MR1616310
Digital Object Identifier: doi:10.1007/BFb0045079
Rokas, A. and Carroll, S. B. (2005). More genes or more taxa? The relative contribution of gene number and taxon number to phylogenetic accuracy. Mol. Biol. Evol. 22 1337--1344.
Semple, C. and Steel, M. (2003). Phylogenetics. Oxford Univ. Press.
Mathematical Reviews (MathSciNet): MR2060009
Zentralblatt MATH: 1043.92026
Steel, M. A., Goldstein, L. and Waterman, M. S. (1996). A central limit theorem for the parsimony length of trees. Adv. in Appl. Probab. 28 1051--1071.
Mathematical Reviews (MathSciNet): MR1418246
Digital Object Identifier: doi:10.2307/1428164
JSTOR: links.jstor.org
Zentralblatt MATH: 0872.60016
Steel, M. A., Hendy, M. D. and Penny, D. (1998). Reconstructing phylogenies from nucleotide pattern frequencies---a survey and some new results. Discrete Appl. Math. 88 367--396.
Mathematical Reviews (MathSciNet): MR1658533
Digital Object Identifier: doi:10.1016/S0166-218X(98)00080-8
Zentralblatt MATH: 0940.92018
Steel, M. and Székely, L. A. (2006). On the variational distance of two trees. Technical Report 05:09, Industrial Mathematics Institute, Univ. South Carolina. Available at http://www.math.sc.edu/~IMI/technical/tech05.html.
Mathematical Reviews (MathSciNet): MR2260073
Digital Object Identifier: doi:10.1214/105051606000000196
Project Euclid: euclid.aoap/1159804991
Zentralblatt MATH: 1111.62111
Tuffley, C. and Steel, M. A. (1997). Modelling the covarion hypothesis of nucleotide substitution. Math. Biosci. 147 63--91.
Mathematical Reviews (MathSciNet): MR1604518
Digital Object Identifier: doi:10.1016/S0025-5564(97)00081-3
Zentralblatt MATH: 0897.92025
The Annals of Applied Probability