Improving genome rearrangement phylogeny using sequence-S parsimony

Proceedings - BIBE 2005: 5th IEEE Symposium on Bioinformatics and Bioengineering

Volumn 2005, Issue , 2005, Pages 137-144

  Tang, Jijun ^a   Wang, Li San ^b  

^a University of South Carolina   (United States)

^b UNIVERSITY OF PENNSYLVANIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHMS; COMPUTER SIMULATION; COMPUTER SOFTWARE; ITERATIVE METHODS; MUTAGENESIS; POLYNOMIALS; PROBLEM SOLVING; TREES (MATHEMATICS);

GENOME REARRANGEMENTS; PARSIMONY; PHYLOGENY; POLYNOMIAL TIME;

GENES;

EID: 33751166381     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/BIBE.2005.39     Document Type: Conference Paper

References (27)

1. D. Bader, B. Moret, and M. Yan. A fast linear-time algorithm for inversion distance with an experimental comparison. J. Comput. Biol., 8(5):483-491, 2001.
2. M. Blanchette, G. Bourque, and D. Sankoff. Break-point phytogenies. In S. Miyano and T. Takagi, editors, Genome Informatics 1907, pages 25-34. Univ. Academy Press, 1997.
3. M. Blanchette and D. Sankoff. The median problem for breakpoints in comparative genomics. In Proc. 3rd Int'l Conf. Computing and Combinatorics (COCOON'97), volume 1276 of Lecture Notes in Computer Science, pages 251-263, Springer Verlag, 1997.
4. J. Boore, T. Collins, D. Stanton, L. Daehler, and W. Brown. Deducing the pattern of arthropod phylogeny from mitochondrial DNA rearrangements. Nature, 376:163-165, 1995.
5. D. Bryant. A lower bound for the breakpoint phylogeny problem. In R. Giancarlo and D. Sankoff, editors, Proc. 11th Ann. Symp. Combinatorial Pattern Matching CPM'00, pages 235-247, Springer, 2000.
6. A. Caprara. On the practical solution of the reversal median problem. In Proc. 1st Int'l Workshop Algs. in Bioinformatics (WABI'01), volume 2149 of Lecture Notes in Computer Science, pages 238-251. Springer Verlag, 2001.
7. M. Cosner, R. Jansen, B. Moret, L. Raubeson, L. Wang, T. Warnow, and S. Wyman. An empirical comparison of phylogenetic methods on chloroplast gene order data in Campanulaceae. In D. Sankoff and J. Nadeau, editors, Comparative Genomics, pages 99-122. Kluwer Academic Publishers, 2000.
8. W. Day. Computationally difficult parsimony problems in phylogenetic systematics. Journal of Theoretical Biology, 103:429-438, 1983.
9. S. Downie and J. Palmer. Use of chloroplast DNA rearrangements in reconstructing plant phylogeny. In P. Soltis, D. Soltis, and J. Doyle, editors, Plant Molecular Systematics, pages 14-35. Chapman and Hall, 1992.
10. W. Fitch. Toward defining the course of evolution: minimum change for a specific tree topology. Systematic. Zoology, 20:406-416, 1971.
11. M. Garey and D. Johnson. Computers and Intractability: A Guide to the Theory of NPCompleteness. Freeman Publisher, 1979.
12. S. Kumar. Minimum evolution trees. Mol. Biol. Evol., 15:584-593, 1996.
13. B. Moret, A. Siepel, J. Tang, and T. Liu. Inversion medians outperform breakpoint medians in phylogeny reconstruction from gene-order data. In Proc. 2nd Int'l Workshop Algs. in Bioinformatics (WABI'02), 2452 of Lecture Notes in Computer Science, pages 521-536. Springer Verlag, 2002.
14. B. Moret, J. Tang, L.-S. Wang, and T. Warnov Steps toward accurate reconstructions of phylogenies from gene-order data. J. Comput. Syst. Sci., 65(3):5 2002.
15. B. Moret, L.-S. Wang, T. Warnow, and S. Wyman. New approaches for reconstructing phylogenies from gene-order data. In Proc. 9th Int'l Conf. on Intelligent Systems for Mol. Biol. (ISMB'01), volume 17 of Bioinformatics, pages S165-S173, 2001.
16. B. Moret, S. Wyman, D. Bader, T. Warnow M. Yan. A new implementation and detailed study of breakpoint analysis. In Proc. 6th Pacific Symp. on Biocomputing (PSB'01), pages 583-594. World Scientific Pub., 2001.
17. J. Palmer. Chloroplast and mitochondrial genome evolution in land plants. In R. Herrmann, editor, Cell Organelles, pages 99-133. Springer Verlag, 1992.
18. L. Raubeson and R. Jansen. Chloroplast DNA evidence on the ancient evolutionary split in vascular land plants. Science, 255:1697-1699, 1992.
19. A. Rokas and P. Holland. Rare genomic changes as a tool for phylogenetics. Trends in Ecol. and Evol., 15:454-459, 2000.
20. N. Saitou and M. Nei. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol., 4:406-425, 1987.
21. M. Sanderson. r8s software package. http://loco.ucdavis.edu/r8s/r8s.html.
22. D. Sankoff and M. Blanchette. Multiple genome rearrangement and breakpoint phylogeny. J. Comput. Biol., 5:555-570, 1998.
23. C. Semple and M. Steel. Phylogenetics. Oxford University Press, 2003.
24. J. Tang and B. Moret. Scaling up accurate phylogenetic reconstruction from gene-order data. In Proc. 11th Int'l Conf. on Intelligent Systems for Mol. Biol. (ISMB'03), volume 19 of Bioinformatics, p i305-i312. Oxford U. Press, 2003.
25. th IEEE Symp. on Bioinformatics and Bioengineering BIBE'04, pages 592-599. IEEE Piscataway, NJ, 2004.
26. L.-S. Wang, R. Jansen, B. Moret, L. Raubeson, and T. Warnow. Fast phylogenetic methods for genome rearrangement evolution: An empirical study. In Proc. 7th Pacific Symp. on Biocomputing (PSB'02), pages 524-535. World Scientific Pub., 2002.
27. L.-S. Wang and T. Warnow. Estimating true evolutionary distances between genomes. In Proc. 33rd Ann. ACM Symp. Theory of Comput. (STOC'01), pages 637-646. ACM Press, New York, 2001.