Using max cut to enhance rooted trees consistency

IEEE/ACM Transactions on Computational Biology and Bioinformatics

Volumn 3, Issue 4, 2006, Pages 323-333

  Snir, Sagi ^a   Rao, Satish ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Phylogenetic trees; Rooted triplets; Semidefinite programming; Supertrees

Indexed keywords

PHYLOGENETIC TREES; ROOTED TRIPLETS; SEMIDEFINITE PROGRAMMING; SUPERTREES;

ALGORITHMS; COMPUTATIONAL COMPLEXITY; DATA STRUCTURES; DECISION MAKING; HEURISTIC METHODS; PROBLEM SOLVING;

TREES (MATHEMATICS);

THUJA;

ALGORITHM; ARTICLE; BIOLOGICAL MODEL; COMPUTER SIMULATION; DNA SEQUENCE; EVOLUTION; METHODOLOGY; MOLECULAR EVOLUTION; PHYLOGENY; POPULATION GENETICS;

ALGORITHMS; COMPUTER SIMULATION; EVOLUTION; EVOLUTION, MOLECULAR; GENETICS, POPULATION; MODELS, GENETIC; PHYLOGENY; SEQUENCE ANALYSIS, DNA;

EID: 33845652502     PISSN: 15455963     EISSN: None     Source Type: Journal    
DOI: 10.1109/TCBB.2006.58     Document Type: Conference Paper

References (27)

1. S. Arora, S. Rao, and U. Vazirani, "Expander Flows, Geometric Embeddings and Graph Partitioning," Proc. Symp. Foundations of Computer Science, 2004.
2. 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. Computing, vol. 10, no. 3, pp. 405-421, 1981.
3. B.R. Baum, "Combining Trees as a Way of Combining Data Sets for Phylogenetic Inference," Taxon, vol. 41 pp. 3-10, 1992.
4. A. Ben-Dor, B. Chor, D. Graur, R. Ophir, and D. Pelleg, "Constructing Phylogenies from Quartets: Elucidation of Eutherian Superordinal Relationships," J. Computational Biology, vol. 5, no. 3, pp. 377-390, 1998.
5. D. Bryant, "Hunting for Trees, Building Trees and Comparing Trees: Theory and Method in Phylogenetic Analysis," PhD thesis, Dept. of Math., Univ. of Canterbury, New Zealand, 1997.
6. D.J. Bryant and M.A. Steel, "Extension Operations on Sets of Leaf-Labelled Trees," Advances in Applied Math., vol. 16, no. 4, pp. 425-453, 2000.
7. M. Cardillo, O.R.P. Bininda-Emonds, E. Boakes, and A. Purvis, "A Species-Level Phylogenetic Supertree of Marsupials," J. Zoology, vol. 264, no. 1, pp. 11-31, 2004.
8. D. Chen, O. Eulenstein, D. Fernandez-Baca, and M. Sanderson, "Supertrees by Flipping," Proc. Int'l Computing and Combinatorics Conf. (COCOON), 2002.
9. O. Eulenstein, D. Chen, J.G. Burleigh, D. Fernandez-Baca, and M.J. Sanderson, "Performance of Flip Supertrees with a Heuristic Algorithm," Systematic Biology, vol. 53, no. 2, pp. 299-308, 2004.
10. P. Erdos, M. Steel, L. Szekely, and T. Warnow, "A Few Logs Suffice to Build (Almost) All Trees (I)," Random Structures and Algorithms, vol. 14, pp. 153-184, 1999.
11. C.M. Fiduccia and R.M. Mattheyses, "A Linear Time Heuristic for Improving Network Partitions," Proc. Design Automation Conf., pp. 175-181, 1982.
12. M.X. Goemans and D.P. Williamson, "Improved Approximation Algorithms for Maximum Cut and Satisfiability Problems Using Semidefinite Programming," J. ACM, vol. 42, no. 6, pp. 1115-1145, Nov. 1995.
13. M.R. Henzinger, V. King, and T. Warnow, "Constructing a Tree from Homeomorphic Subtrees, with Applications to Computational Evolutionary Biology," Proc. ACM-SIAM Symp. Discrete Algorithms (SODA), pp. 333-340, 1996.
14. D. Huson, S. Nettles, and T. Warnow, "Disk-Covering, a Fast Converging Method for Phylogenetic Tree Reconstruction," J. Computational Biology, no. 6, pp. 369-386, 1999.
15. B.W. Kernighan and S. Lin, "An Encient Heuristic Procedure for Partitioning Graphs," The Bell Systems Technical J., vo. 29, no. 2, pp. 291-307, 1970.
16. E. Mossel, "Distorted Metrics on Trees and Phylogenetic Forests," submitted, 2005.
17. S. Moran, S. Rao, and S. Snir, "Using Semi-Definite Programming to Enhance Supertree Resolvability," Proc. Fifth Int'l Workshop Algorithms in Bioinformatics (WABI), pp. 89-103, Oct. 2005.
18. S. Moran and S. Snir, "Convex Recoloring of Strings and Trees: Definitions, Hardness Results and Algorithms," J. Computer and System Sciences, 2005.
19. R.D.M. Page, "Modified Mincut Supertrees," Proc. Int'l Workshop Algorithms in Bioinformatics (WABI), R. Guigo and D. Gusfield, eds., 2002.
20. W. Piel, M. Donoghue, and M. Sanderson, "TreeBASE: A Database of Phylogenetic Knowledge," Nat'l Inst. for Environmental Studies, Tsukuba, Japan, 2002, http://www.treebase.org.
21. M.A. Ragan, "Matrix Representation in Reconstructing Phylogenetic-Relationships among the Eukaryotes," Biosystems, vol. 28, pp. 47-55, 1992.
22. K. Rice, M. Donoghue, and R. Olmstead, "Analyzing Large Datasets: rbcl 500 Revisited," Systematic Biology, vol. 46, no. 4, pp. 554-563, 1997.
23. M. Steel, A. Dress, and S. Boker, "Simple but Fundamental Limitations on Supertree and Consensus Tree Methods," Systematic Biology, vol. 49, pp. 363-368, 2000.
24. C. Semple and M. Steel, "A Supertree Method for Rooted Trees," Discrete Applied Math., vol. 103, pp. 147-158, 2000.
25. M. Steel, "The Complexity of Reconstructing Trees from Qualitative Characters and Subtress," J. Classification, vol. 9, no. 1, pp. 91-116, 1992.
26. M. Stoer and F. Wagner, "A Simple Min-Cut Algorithm," J. ACM, vol. 44, pp. 585-591, 1997.
27. L. Vandenberghe and S. Boyd, "Semidefinite Programming," SIAM Rev., vol 38, no. 1, pp. 49-95, 1996.