A robust model for finding optimal evolutionary trees extended abstract

Proceedings of the Annual ACM Symposium on Theory of Computing

Volumn Part F129585, Issue , 1993, Pages 137-145

  Farach, Martin ^a   Kannan, Sampath ^b   Warnow, Tandy ^c  

^a RUTGERS UNIVERSITY   (United States)

^b UNIVERSITY OF ARIZONA   (United States)

^c SANDIA NATIONAL LABORATORIES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTATION THEORY; EVOLUTIONARY ALGORITHMS; MATRIX ALGEBRA; OPTIMIZATION; POLYNOMIAL APPROXIMATION; POLYNOMIALS; ALGORITHMS; APPROXIMATION THEORY; COMPUTATIONAL COMPLEXITY; COMPUTATIONAL METHODS; MATHEMATICAL MODELS;

APPROXIMATE SOLUTION; COMPUTATIONAL BIOLOGY; DISTANCE FUNCTIONS; EXTENDED ABSTRACTS; OPTIMIZATION PROBLEMS; POLYNOMIAL-TIME ALGORITHMS; THE STANDARD MODEL; UPPER AND LOWER BOUNDS;

TREES (MATHEMATICS);

COMPUTATIONAL BIOLOGY; OPTIMAL EVOLUTIONARY TREES; PHYLOGENETIC TREE;

EID: 0027307380     PISSN: 07378017     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1145/167088.167132     Document Type: Conference Paper

References (40)

1. A.V. Aho, Y. Sagiv, T.G. Szymanski, and J.D. Ullman, Inferring a tree from lowest common ancestors with an application to the optimization of relational expressions, SIAM J. of Computing, vol 10, no. 3, 1981.
2. S.F. Altschul, Amino acid substitution matrices from an information theoretic perspective., J. Mol. Biol. 219: 555-565, 1991.
3. W. Beyer, M. Stein, T. Smith and S. Ulam, A molecular sequence metric and evolutionary trees, Math. Biosci., 19:9-25.
4. H. Bodlaender, M. Fellows, and T. Warnow, Two strikes against perfect phylogeny, appeared, Proceedings, International Congress on Automata and Language Processing (ICALP), Vienna, Austria, July 1992.
5. P. Buneman, Mathematics in the Archeoologi- cal and Historical Sciences, (F.R. Hobson, D. G. Kendall and P. Tautu, eds) p. 387, Edinburgh: University Press.
6. L. Cavalli-Sforza and A. Edwards, Phyloge- netic analysis models and estimation procedures, Evolution, 32:550-70, 1967.
7. T. Cormen, C Leiserson, and R. Rivest, Introduction to Algorithms, MIT Press, 1990.
8. J. Culberson and P. Rudnicki, A fast algorithm for constructing trees from distance matrices, Information Processing Letters, 30 (1989), pp. 215-220.
9. W.H.E. Day, Computational complexity of inferring phylogenies from dissimilarity matrices, Bulletin of Mathematical Biology, Vol. 49, No. 4, pp. 461-467, 1987.
10. M. Dayhoff and R. Eck, Atlas of Protein Sequence and Structure 1967-68, pp. 307. Silver Spring, Maryland: Natl. Biomed. Res. Found.
11. Trees and Hierarchical Structures, Lecture Notes in Biomathematics, ed. Dress and Von Haessler, Springer-Verlag, 1987.
12. M. Farach, S. Kannan, and T. Warnow, A Robust Model for Finding Optimal Evolutionary Trees, to appear in Algorithmica.
13. J.S. Farris, Estimating phylogenetic trees from distance matrices, Am. Nat., 106, pp. 645-668, 1972.
14. J. Felsenstein, Numerical methods for inferring evolutionary trees, The Quarterly Review of Biology, Vol. 57, No. 4, Dec. 1982.
15. J. Felsenstein, Phylogenies from molecular sequences: inference and reliability, Annual Rev. Genet. 1988, 22:521-65.
16. W. Fitch, A Non-sequential method for constructing trees and hierarchical classifications, J. of Molecular Evolution, 1981.
17. W.M. Fitch and E. Margoliash, The construction of phylogenetic trees, Science 155:29-94, 1976.
18. M.R. Garey and D.S. Johnson, Computers and Intractability, 1979, New York: W.H. Freeman and Company, 340 pp., 1979.
19. G.H. Gonnet, M.A. Cohen, and S.A. Ben-ner, Exhaustive matching of the entire protein sequence database, Science 256:14431445, 1992.
20. D. Harel and R. Tarjan, Fast Algorithm for Finding Nearest Common Ancestors, SI AM J. Comput. 13(2):338-355, 1984.
21. J. Hein, An optimal algorithm to reconstruct trees from additive distance matrices, Bulletin of Mathematical Biology, Vol. 51, No. 5, pp. 597-603, 1989.
22. J. Hein, A new method that simultaneously aligns and reconstructs ancestral sequences for any number of homologous sequences, when the phytogeny is given, Mol. Biol. Evol. 6(6):649-668 1989.
23. J. Hein, A tree reconstruction method that is economical in the number of pairwise compar-isons used, Mol. Biol. Evol. 6(6), pp. 669-684, 1989.
24. C.J. Jardine, N. Jardine, and R. Sibson, The Structure and Construction of Taxonomic Hi-erarchies, Mathematical Biosciences, 1, 173179, 1967.
25. T.H. Jukes and C.R. Cantor, Evolution of protein molecules in Mammalian Protein Metabolism, (H.N Munro, ed.), Academic Press, New York, pp. 21-132, 1969.
26. S. Kannan, E. Lawler, and T. Warnow, Determining the evolutionary tree, Proc. First Annual ACM-SIAM Symp. on Discrete Algorithms, San Francisco, Jan. 1990.
27. S. Kannan and T. Warnow, Using Experiments to Infer Evolutionary Trees, manuscript.
28. M. Krivanek, The complexity of ultrametric partitions on graphs, Info. Proc. Letters, Vol. 27 No. 5, (1988) 265-270.
29. W.-H. Li, Simple method for constructing phylogenetic trees from distance matrices., Proc. Natl. Acad, of Sciences, USA, 78:1085-89.
30. C. Lund and M. Yannakakis, On the hardness of approximating minimization problems, 1992, manuscript.
31. W. Miller and E.W. Myers, Sequence Comparison with Concave Weighting Functions, Bull. Math. Bio. Vol. 50 (2) (1988) 97-120.
32. N. Saitou and M. Nei, The neighbor-joining method: A new method for reconstructing phylogenetic trees, Mol. Biol. Evol. 4:406-25, 1987.
33. D. Sankoff, Minimum mutation trees of sequences, SIAM J. of Applied Math, 28 (1975) pp. 35-42.
34. R. Sokal and P. Sneath, Numerical Taxonomy,, San Francisco: Freeman, 359. pp., 1963.
35. M.A. Steel, The complexity of reconstructing trees from qualitative characters and subtrees, Journal of Classification, Vol. 9, 1992.
36. E. Sweedyk and T. Warnow, The Optimal Tree Alignment Problem is Hard, manuscript, 1992.
37. R.E. Tarjan, Sensitivity Analysis of Minimum Spanning Trees and Shortest Path Trees, Information Processing Letters 14(1):30-33, 1982.
38. Y. Tateno, M. Nei, F. Tajima, Accuracy of estimated phylogenetic trees from molecular data. I: Distantly related trees, J. Mol. Evol., 18:387-404.
39. M.S. Waterman, T.F. Smith, M. Singh, and W.A. Beyer, Additive evolutionary trees, J. Theor. Biol., 64, pp. 199-213, 1977.
40. W.J. Wilbur, On the PAM matrix model of protein evolution, Mol. Biol. Evol. 2:434-447, 1985.