The asymmetric median tree - A new model for building consensus trees

Discrete Applied Mathematics

Volumn 71, Issue 1-3, 1996, Pages 311-335

  Phillips, Cynthia ^a   Warnow, Tandy J ^b  

^a SANDIA NATIONAL LABORATORIES   (United States)

^b UNIVERSITY OF PENNSYLVANIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 0042014724     PISSN: 0166218X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0166-218X(96)00071-6     Document Type: Article

References (36)

1. E. Adams III, Consensus techniques and the comparison of taxonomic trees, Syst. Zoology 21 (1972) 390-397.
2. E. Adams III, N-trees as nestings : complexity, similarity, and consensus, J. Classification 3 (1986) 299-317.
3. J. Barthélemy and F. Janowitz, A formal theory of consensus, SIAM J. Discrete Math. 3 (1991) 305-322.
4. J. Barthélemy and F. McMorris, The median procedure for n-Trees, J. Classification 3: (1986) 329-334.
5. M. Bellare and M. Sudan, Improved non-approximability results, Proceedings of the 26th Annual ACM Symposium on Theory of Computing, Montreal, (ACM, New York) 184-193.
6. D. Bryant, Hunting for binary trees in binary character sets: efficient algorithms for extraction, enumeration, and optimization, Research Report no. 124, Department of Mathematics and Statistics, Canterbury University, Christchurch, New Zealand, (April 1995).
7. W.H.E. Day, Optimal algorithms for comparing trees with labelled leaves, J. Classification 2 (1985) 7-28.
8. W.H.E. Day and D. Sankoff, Computational complexity of inferring phylogenies by compatibility, Syst. Zoology 35 (1986) 224-229.
9. G.F. Estabrook, C.S. Johnson, Jr. and F.R. McMorris, An idealized concept of the true cladistic character, Math. Biosci. 23 (1975) 263-272.
10. G.F. Estabrook, C.S. Johnson, Jr. and F.R. McMorris, A mathematical foundation for the analysis of cladistic character compatibility, Math. Biosci. 29 (1976) 181-187.
11. G.F. Estabrook, C.S. Johnson, Jr. and F.R. McMorris, An algebraic analysis of cladistic characters, Discrete Math. 16 (1976) 141-147.
12. G.F. Estabrook and F.R. McMorris, When is one estimate of evolutionary relationships a refinement of another? J. Math. Biosci. 10 (1980) 327-373.
13. M. Farach, T. Przytycka and M. Thorup, On the agreement of many trees, Inform. Process. Lett., to appear.
14. M. Farach and M. Thorup, Optimal evolutionary tree comparisons by sparse dynamic programming, Proceedings of the 35th annual IEEE Foundations of Computer Science (1994) 770-779; SIAM J. on Computing, to appear.
15. M. Farach and M. Thorup, Optimal evolutionary tree comparisons by sparse dynamic programming, Proceedings of the 35th annual IEEE Foundations of Computer Science (1994) 770-779; SIAM J. on Computing, to appear.
16. J. Felsenstein, personal communication.
17. J. Felsenstein, Cases in which parsimony or compatibility methods will be positively misleading, Syst. Zoology 27 (1978) 401-410.
18. M.R. Garey and D.S. Johnson, Computers and Intractability: A Guide to the Theory of NP-Completeness (W.H. Freeman and Company, New York, 1979).
19. D. Gusfield, Efficient algorithms for inferring evolutionary trees, Networks 21 (1991) 19-28.
20. M. Hendy, The relationship between simple evolutionary tree models and observable sequence data, Syst. Zoology 38 (1989) 310-321.
21. M. Hendy and D. Penny, A framework for the quantative study of evolutionary trees, Syst. Zoology 38 (1989) 297-309.
22. 2.5) algorithm for maximum matching in bipartite graphs, SIAM J. Comput. (1975) 225-231.
23. D.S. Johnson, A catalog of complexity classes, in: Algorithms and Complexity, Handbook of Theoretical Computer Science, Vol. A (Elsevier, Amsterdam, 1990) 67-161.
24. S. Kannan, S. Yooseph and T. Warnow, Computing the local consensus of trees, Proceedings of the 1995 ACM/SIAM Symposium on Discrete Algorithms (SODA) (1995).
25. M. Kao, Tree contractions and evolutionary trees, submitted.
26. D. Keselman and A. Amir, Maximum agreement subtree in a set of evolutionary trees - metrics and efficient algorithms, Proceedings of the 35th Annual IEEE Foundations of Computer Science (1994) 758-769.
27. F.R. McMorris and M. Steel, The complexity of the median procedure for binary trees, Proceedings of the 4th Conference of the International Federation of Classification Societies, Paris, 1993, Studies in Classification, Data Analysis, and Knowledge Organization (Springer, Berlin, 1993), to be published.
28. G. Nelson, Cladistic analysis and synthesis: Principles and definitions, with a historical note on Adanson's Familles des Plantes (1763-1764), Syst. Zoology 28 (1979) 1-21.
29. G. Nelson and N.I. Platnick, Systematics and Biogeography: Cladistics and Vicariance (Columbia Univ. Press, New York, 1981).
30. R.D.M. Page, Tracks and trees in the antipodes: a reply to Humphries and seberg, Syst. Zoology 39 (1990) 288-299.
31. R.D.M. Page, Genes, Organisms and areas: The problem of multiple lineages, Syst. Bio. 42 (1993) 77-84.
32. R.D.M. Page, Reconciled trees and Cladistic analysis of historical associations between genes, organisms, and areas, manuscript (1993).
33. N. Saitou and M. Nei, The neighbor-joining method: a new method for reconstructing evolutionary trees, Mol. Biol. Evol. 4 (1987) 406-425.
34. M.A. Steel and T.J. Warnow, Kaikoura tree theorems: computing the maximum agreement subtree, Inform. Process. Lett. 48 (1993) 72-82.
35. H.T. Wareham, An efficient algorithm for computing M1 consensus trees, Honors Dissertation, Department of Computer Science, Memorial University of Newfoundland, St. John's, Newfoundland (1985).
36. T.J. Warnow, Tree compatibility and inferring evolutionary history, J. Algorithms 16 (1991) 388-407.