Efficiently finding the most parsimonious phylogenetic tree via linear programming

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 4463 LNBI, Issue , 2007, Pages 37-48

  Sridhar, Srinath ^a   Lam, Fumei ^b   Blelloch, Guy E ^a   Ravi, R ^b   Schwartz, Russell ^c  

^a Carnegie Mellon University   (United States)

^b CARNEGIE MELLON UNIVERSITY   (United States)

^c CARNEGIE MELLON UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CHROMOSOMES; COMPUTATIONAL METHODS; CONSTRAINT THEORY; DNA; HEURISTIC METHODS; LINEAR PROGRAMMING; PROBLEM SOLVING;

COMPUTATIONAL BIOLOGY; DATASETS; INTEGER LINEAR PROGRAMMING FORMULATION; PARSIMONIOUS PHYLOGENETIC TREES;

TREES (MATHEMATICS);

EID: 34547439745     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-540-72031-7_4     Document Type: Conference Paper

References (35)

1. R. Agarwala and D. Fernandez-Baca. A polynomial-time algorithm for the perfect phylogeny problem when the number of character states is fixed. SIAM Journal on Computing, 23:1216-1224, 1994.
2. V. Bafna, D. Gusfield, G. Lancia, and S. Yooseph. Haplotyping as perfect phylogeny: A direct approach. Journal of Computational Biology, 10:323-340, 2003.
3. H. J. Bandelt, P. Forster, B. C. Sykes, and M. B. Richards. Mitochondrial portraits of human populations using median networks. Genetics, 141:743-753, 1989.
4. J. Barthélemy. From copair hypergraphs to median graphs with latent vertices. Discrete Math, 76:9-28, 1989.
5. J. E. Beasley. An algorithm for the Steiner problem in graphs. Networks, 14:147-159, 1984.
6. G. E. Blelloch, K. Dhamdhere, E. Halperin, R. Ravi, R. Schwartz, and S. Sridhar. Fixed parameter tractability of binary near-perfect phylogenetic tree reconstruction. International Colloquium on Automata, Languages and Programming, 2006.
7. P. Buneman. The recovery of trees from measures of dissimilarity. Mathematics in the Archeological and Historical Sciences, F. Hodson et al., Eds., pages 387-395, 1971.
8. X. Cheng and D. Z. Du (Eds.). Steiner Trees in Industry. Springer, 2002.
9. The ENCODE Project Consortium. The ENCODE (ENCyclopedia Of DNA Elements) Project. Science, 306(5696):636-640, 2004.
10. Lindblad-Toh et al. Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature, 438(7069):803-819, 2005.
11. Lindblad-Toh K et al. Large-scale discovery and genotyping of single-nucleotide polymorphisms in the mouse. Nature Genetics, pages 381-386, 2000.
12. J. Felsenstein. PHYLIP (Phylogeny Inference Package) version 3.6. distributed by the author, Department of Genome Sciences, University of Washington, Seattle, 2005.
13. D. Fernandez-Baca and J. Lagergren. A polynomial-time algorithm for near-perfect phylogeny. SIAM Journal on Computing, 32:1.115-1127, 2003.
14. L. R. Foulds and R. L. Graham. The Steiner problem in phylogeny is NP-complete. Advances in Applied Mathematics, 3, 1982.
15. Michael R. Garey and David S. Johnson. Computers and Intractability: A Guide to the Theory of NP-Completeness. W. H. Freeman & Co., New York, NY, USA, 1979.
16. D. Gusfield. Efficient algorithms for inferring evolutionary trees. Networks, 21:19-28, 1991.
17. D. Gusfield. Haplotyping by pure parsimony. Combinatorial Pattern Matching, 2003.
18. D. Gusfield and V. Bansal. A fundamental decomposition theory for phylogenetic networks and incompatible characters. Research in Computational Molecular Biology, 2005.
19. A. Helgason, G. Palsson, H. S. Pedersen, E. Angulalik, E. D. Gunnarsdottir, B. Yngvadottir, and K. Stefansson. mtDNA variation in Inuit populations of Greenland and Canada: migration history and population structure. American Journal of Physical Anthropology, 130:123-134, 2006.
20. F. K. Hwang, D. S. Richards, and P. Winter. The Steiner Tree Problem, volume 53. Annals of Discrete Mathematics, 1992.
21. The International HapMap Consortium. The International HapMap Project. www.hapmap.org. Nature, 426:789-796, 2005.
22. S. Kannan and T. Warnow. A fast algorithm for the computation and enumeration of perfect phylogenies. SIAM Journal on Computing, 26:1749-1763, 1997.
23. C. M. Jr. Lewis, R.Y. Tito, B. Lizarraga, and A. C Stone. Land, language, and loci: mtDNA in Native Americans and the genetic history of Peru. American Journal of Physical Anthropology, 127:351-360, 2005.
24. N. Maculan. The Steiner problem in graphs. Annals of Discrete Mathematics, 31:185-212, 1987.
25. M. Merimaa, M. Liivak, E. Heinaru, J. Truu, and A. Heinaru. Functional coadaption of phenol hydroxylase and catechol 2,3-dioxygenase genes in bacteria possessing different phenol and p-cresol degradation pathways. Eighth Symposium on Bacterial Genetics and Ecology, 31:185-212, 2005.
26. Sharma S, Saha A, Rai E, Bhat A, and Bamezai R. Human mtDNA hypervariable regions, HVR I and II, hint at deep common maternal founder and subsequent maternal gene flow in Indian population groups. American Journal of Human Genetics, 50:497-506, 2005.
27. N. Saitou and M. Nei. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution, 4(4):406-425, 1987.
28. C. Semple and M. Steel. Phylogenetics. Oxford University Press, 2003.
29. The Chimpanzee Sequencing and Analysis Consortium. Initial sequence of the chimpanzee genome and comparison with the human genome. Nature, 437(7055):69-87, 2005.
30. Elizabeth M. Smigielski, Karl Sirotkin, Minghong Ward, and Stephen T. Sherry. dbSNP: a database of single nucleotide polymorphisms. Nucleic Acids Research, 28(1):352-355, 2000.
31. S. Sridhar, G. E. Blelloch, R. Ravi, and R. Schwartz. Optimal imperfect phylogeny reconstruction and haplotyping. Computational Systems Bioinformatics, 2006.
32. S. Sridhar, K. Dhamdhere, G. E. Blelloch, E. Halperin, R. Ravi, and R. Schwartz. Simple reconstruction of binary near-perfect phylogenetic trees. International Workshop on Bioinformatics Research and Applications, 2006.
33. A. C. Stone, R. C. Griffiths, S. L. Zegura, and M. F. Hammer. High levels of Y-chromosome nucleotide diversity in the genus Pan. Proceedings of the National Academy of Sciences USA, pages 43-48, 2002.
34. Thierry Wirth, Xiaoyan Wang, Bodo Linz, Richard P. Novick, J. Koji Lum, Martin Blaser, Giovanna Morelli, Daniel Falush, and Mark Achtman. Distinguishing human ethnic groups by means of sequences from Helicobacter pylori: Lessons from Ladakh. Proceedings of the National Academy of Sciences USA, 101(14):4746-4751, 2004.
35. R. T. Wong. A dual ascent approach for Steiner tree problems on a directed graph. Mathematical Programming, 28:271-287, 1984.