Constructing evolutionary trees in the presence of polymorphic characters

SIAM Journal on Computing

Volumn 29, Issue 1, 1999, Pages 103-131

  Bonet, Maria ^a   Phillips, Cynthia ^b   Warnow, Tandy ^c   Yooseph, Shibu ^c  

^a UNIVERSITAT POLITÈCNICA DE CATALUNYA   (Spain)

^b SANDIA NATIONAL LABORATORIES   (United States)

^c UNIVERSITY OF PENNSYLVANIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHMS; COMPUTATIONAL COMPLEXITY; COMPUTATIONAL LINGUISTICS; DATA REDUCTION; MATHEMATICAL MORPHOLOGY;

EVOLUTIONARY TREES; POLYMORPHISMS;

TREES (MATHEMATICS);

EID: 0342298647     PISSN: 00975397     EISSN: None     Source Type: Journal    
DOI: 10.1137/S0097539796324636     Document Type: Article

References (40)

1. R. AGARWALA AND D. FERNÁNDEZ-BACA, A polynomial-time algorithm for the perfect phylogeny problem when the number of character states is fixed, SIAM J. Comput., 23 (1994), pp. 1216-1224.
2. R. AGARWALA AND D. FERNÁNDEZ-BACA, Fast and Simple Algorithms for Perfect Phylogeny and Triangulating Colored Graphs, Technical report TR94-51, DIMACS, to appear in special issue on algorithmic aspects of computational biology, Internat. J. Found. Comput. Sci.
3. S. ARNBORG, D. CORNEIL, AND A. PROSKUROWSKI, Complexity of finding embeddings in a k-Tree, SIAM J. Alg. Discrete Methods. 8 (1987), pp. 277-284.
4. H. BODLAENDER, M. FELLOWS, AND T. WARNOW, Two strikes against perfect phylogeny, in Proc. 19th International Colloquium on Automata, Languages, and Programming, Lecture Notes in Comput. Sci., Springer-Verlag, New York, 1992, pp. 273-283.
5. H. BODLAENDER AND T. KLOKS, A simple linear time algorithm for triangulating three-colored graphs, in Proc. 9th Annual Symposium on Theoretical Aspects of Computer Science, Cachan, France, 1992, pp. 415-423, to appear in J. Algorithms.
6. M. BONET, C. PHILLIPS, T. WARNOW. AND SHIBU YOOSEPH, Constructing evolutionary trees in the presence of polymorphic characters, in Proc. Twenty-Eighth Annual ACM Symposium on Theory of Computing, Philadelphia, 1996, pp. 220-229.
7. P. BUNEMAN, A characterization of rigid circuit graphs, Discrete Math., 9 (1974), pp. 205-212.
8. L. L. CAVALLI-SFORZA, P. MENOZZI, AND A. PIAZZA, The History and Geography of Human Genes, Princeton University Press, Princeton, NJ, 1994.
9. W. H. E. DAY, Computationally difficult parsimony problems in phylogenetic systematics, J. Theoret. Biol., 103 (1983), pp. 429-438.
10. W. H. E. DAY, D. S. JOHNSON, AND D. SANKOFF, The computational complexity of inferring phylogenies by parsimony, Math. Biosci., 81 (1986), pp. 33-42.
11. W. H. E. DAY AND D. SANKOFF, Computational complexity of inferring phylogenies by compatibility, Systematic Zool., 35 (1986), pp. 224-229.
12. A. DRESS AND M. STEEL, Convex tree realizations of partitions, Appl. Math. Lett., 5 (1992), pp. 3-6.
13. G. F. ESTABROOK, Cladistic methodology: A discussion of the theoretical basis for the induction of evolutionary history, Annu. Rev. Ecol. Syst., 3 (1972), pp. 427-456.
14. G. F. ESTABROOK, C. S. JOHNSON, JR., AND F. R. MCMORRIS, An idealized concept of the true cladistic character, Math. Biosci., 23 (1975), pp. 263-272.
15. J. FELSENSTEIN, Alternative methods of phylogenetic inference and their interrelationships, Systematic Zool., 28 (1979), pp. 49-62.
16. W. FITCH, Towards defining the course of evolution: Minimum change for a specified tree topology, Systematic Zool., 20 (1971), pp. 406-416.
17. M. C. GOLUMBIC, Algorithmic Graph Theory and Perfect Graphs, Academic Press, New York, 1980.
18. D. GUSFIELD, Efficient algorithms for inferring evolutionary trees, Networks, 21 (1991), pp. 19-28.
19. R. M. IDURY AND A. A. SCHÄFFER, Triangulating three-colored graphs in linear time and linear space, SIAM J. Discrete Math., 6 (1993), pp. 289-293.
20. R. KARP, Reducibility among combinatorial problems, in Complexity of Computer Computations, R. E. Miller and J. W. Thatcher, eds., Plenum Press, New York, 1972, pp. 85-103.
21. S. KANNAN AND T. WARNOW, Inferring evolutionary history from DNA sequences, SIAM J. Comput., 23 (1994), pp. 713-737.
22. S. KANNAN AND T. WARNOW, Triangulating 3-colored graphs, SIAM J. Discrete Math., 5 (1992), pp. 249-258.
23. S. KANNAN AND T. WARNOW, A fast algorithm for the computation and enumeration of perfect phylogenies, SIAM J. Comput., 26 (1997), pp. 1749-1763.
24. W. J. LE QUESNE, A method of selection of characters in numerical taxonomy, Systematic Zool., 18 (1969), pp. 201-205.
25. W. J. LE QUESNE, Further studies based on the uniquely derived character concept, Systematic Zool., 21 (1972), pp. 281-288.
26. M. F. MICKEVICH AND C. MITTER, Treating polymorphic characters in systematics: A phylogenetic treatment of electrophoretic data, in Advances in Cladistics, V. A. Funk and D. R. Brooks, eds., New York Botanical Garden, New York, 1981, pp. 45-58.
27. F. R. MCMORRIS, T. WARNOW, AND T. WIMER, Triangulating vertex-colored graphs, SIAM J. Discrete Math., 7 (1994), pp. 296-306.
28. M. NEI, Molecular Evolutionary Genetics, Columbia University Press, New York, 1987.
29. A. PROSKUROWSKI, Separating subgraphs in k-trees: Cables and caterpillars, Discrete Math., 49 (1984), pp. 275-285.
30. D. RINGE, personal communication, 1995.
31. D. J. ROSE, On simple characterization of k-trees, Discrete Math., 7 (1974), pp. 317-322.
32. D. J. ROSE, R. E. TARJAN, AND G. S. LUEKER, Algorithmic aspects of vertex elimination on graphs, SIAM J. Comput., 5 (1976), pp. 266-283.
33. A. K. ROYCHOUDHURY AND M. NEI, Human Polymorphic Genes: World Distribution, Oxford University Press, London, UK, 1988.
34. D. SANKOFF AND R. J. CEDERGREN, Simultaneous comparison of three or more sequences related by a tree, in Time Warps, String Edits, and Macromolecules: The Theory and Practice of Sequence Comparison. D. Sankoff and J.B. Kruskal, eds., Addison-Wesley, Reading MA, 1983, pp. 253-263
35. D. SANKOFF AND P. ROUSSEAU, Locating the vertices of a Steiner tree in arbitrary space, Math. Programming, 9 (1975), pp. 240-246.
36. M. A. STEEL, The complexity of reconstructing trees from qualitative characters and subtrees, J. Classification, 9 (1992), pp. 91-116.
37. T. WARNOW, Constructing phylogenetic trees efficiently using compatibility criteria, New Zealand J. Botany, 31 (1993), pp. 239-248.
38. T. WARNOW, Mathematical approaches to comparative linguistics. in Proceedings of the National Academy of Sciences, vol. 94, 1997, pp. 6585-6590.
39. T. WARNOW, D. RINGE, AND A. TAYLOR, A character based method for reconstructing evolutionary history for natural languages, Technical report, Institute for Research in Cognitive Science, 1995, and Proc. ACM/SIAM Symposium on Discrete Algorithms, Atlanta, GA, 1996.
40. J. J. WEINS, Polymorphic characters in phylogenetic Systematics, Systematic Biology, 44 (1995), pp. 482-500.