Quartet-based phylogeny reconstruction from gene orders

Lecture Notes in Computer Science

Volumn 3595, Issue , 2005, Pages 63-73

  Liu, Tao ^a   Tang, Jijun ^b   Moret, Bernard M E ^a  

^a UNIVERSITY OF NEW MEXICO   (United States)

^b University of South Carolina   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHMS; BIOTECHNOLOGY; COMPUTER SOFTWARE; HEURISTIC METHODS; BIOLOGY; COMBINATORIAL MATHEMATICS; COMPUTATIONAL COMPLEXITY; GENES; OPTIMIZATION; TREES (MATHEMATICS);

DIRECT OPTIMIZATION; GENE ORDERS; PHYLOGENY; QUARTET-BASED METHOD; COMPUTER SCIENTISTS; DISTANCE-BASED METHODS; OPTIMIZATION ALGORITHMS; PHYLOGENETIC RECONSTRUCTION; QUARTET BASED METHOD; QUARTET BASED PHYLOGENY; RECURSIVE DECOMPOSITION;

GENES; HEURISTIC METHODS;

EID: 26844462685     PISSN: 03029743     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1007/11533719_9     Document Type: Conference Paper

References (32)

1. V. Berry, T. Jiang, P. Kearney, M. Li, and T. Wareham. Quartet cleaning: improved algorithms and simulations. In Proc. Europ. Symp. Algs. (ESA99), volume 1643 of Lecture Notes in Computer Science, pp. 313-324. Springer Verlag, 1999.
2. M. Blanchette, G. Bourque, and D. Sankoff. Breakpoint phylogenies. In S. Miyano and T. Takagi, editors, Genome Informatics 1997, pp. 25-34. Univ. Academy Press, 1997.
3. D. Bryant, V. Berry, T. Jiang, P. Kearney, M. Li, T. Wareham, and H. Zhang. A practical algorithm for recovering the best supported edges of an evolutionary tree. In Proc. 11th Ann. ACM/SIAM Symp. Discrete Algs. (SODA'00), pp. 287-296. ACM Press, New York, 2000.
4. P. Buneman. The recovery of trees from measures of dissimilarity. Edinburgh University Press, 1971.
5. A. Caprara. Formulations and hardness of multiple sorting by reversals. In Proc. 3rd Ann. Int'l Conf. Comput. Mol. Biol (RECOMB'99), pp. 84-93. ACM Press, New York, 1999.
6. M.E. Cosner, R.K. Jansen, B.M.E. Moret, L.A. Raubeson, L. Wang, T. Warnow, and S.K. Wyman. An empirical comparison of phylogenetic methods on chloroplast gene order data in Campanulaceae. In D. Sankoff and J.H. Nadeau, editors, Comparative Genomics, pp. 99-122. Kluwer Academic Publishers, 2000.
7. S.R. Downie and J.D. Palmer. Use of chloroplast DNA rearrangements in reconstructing plant phylogeny. In P. Soltis, D. Soltis, and J.J. Doyle, editors, Plant Molecular Systematics, pp. 14-35. Chapman and Hall, 1992.
8. P. Erdos, M. A. Steel, L. A. Székely, and T. Warnow. A few logs suffice to build (almost) all trees I. Random Structs. and Algs., 14:153-184, 1997.
9. P. L. Erdos, M. A. Steel, L. A. Székely, and T. Warnow. Constructing big trees from short sequences. In Proc. 24th Int'l Colloq. on Automata, Languages, and Programming (ICALP97), volume 1256 of Lecture Notes in Computer Science. Springer Verlag, 1997.
10. P. L. Erdos, M. A. Steel, L. A. Székely, and T. Warnow. Local quartet splits of a binary tree infer all quartet splits via one dyadic inference rule. Computers and Artif. Intell., 16(2):217-227, 1997.
11. D. Huson, S. Nettles, and T. Warnow. Disk-covering, a fast converging method for phylogenetic tree reconstruction. J. Comput. Biol., 6(3):369-386, 1999.
12. T. Jiang, P.E. Kearney, and M. Li. A polynomial-time approximation scheme for inferring evolutionary trees from quartet topologies and its application. SIAM J. Computing, 30(6): 1942-1961, 2001.
13. P.E. Kearney. The ordinal quartet method. In Proc. 2nd Ann. Int'l Conf. Comput. Mol. Biol. (RECOMB'98), pp. 125-134. ACM Press, New York, 1998.
14. B.M.E. Moret, A.C. 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), volume 2452 of Lecture Notes in Computer Science, pp. 521-536. Springer Verlag, 2002.
15. B.M.E. Moret, J. Tang, L.-S. Wang, and T. Warnow. Steps toward accurate reconstructions of phylogenies from gene-order data. J. Comput. Syst. Sci., 65(3):508-525, 2002.
16. B.M.E. Moret, J. Tang, and T. Warnow. Reconstructing phylogenies from gene-content and gene-order data. In O. Gascuel, editor, Mathematics of Evolution and Phylogeny, pp. 321-352. Oxford University Press, 2005.
17. J.D. Palmer. Chloroplast and mitochondrial genome evolution in land plants. In R. Herrmann, editor, Cell Organelles, pp. 99-133. Springer Verlag, 1992.
18. L.A. Raubeson and R.K. Jansen. Chloroplast DNA evidence on the ancient evolutionary split in vascular land plants. Science, 255:1697-1699, 1992.
19. A. Rokas and P.W.H. Holland. Rare genomic changes as a tool for phylogenetics. Trends in Ecol. and Evol., 15:454-459, 2000.
20. U. Roshan, B.M.E. Moret, T. Warnow, and T.L. Williams. Performance of supertree methods on various dataset decompositions. In O.R.P. Bininda-Edmonds, editor, Phylogenetic Supertrees: Combining information to reveal the Tree of Life, pp. 301-328. Kluwer Academic Publishers, 2004.
21. N. Saitou and M. Nei. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol., 4:406-425, 1987.
22. D. Sankoff and M. Blanchette. 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, pp. 251-264. Springer Verlag, 1997.
23. D. Sankoff and M. Blanchette. Multiple genome rearrangement and breakpoint phylogeny. J. Comput. Biol., 5:555-570, 1998.
24. K. St. John, T. Warnow, B.M.E. Moret, and L. Vawter. Performance study of phylogenetic methods: (unweighted) quartet methods and neighbor-joining. J. Algorithms, 48(1): 173-193, 2003. A preliminary version appeared in SODA'01, pp. 196-205.
25. K. Strimmer and A. von Haeseler. Quartet puzzling: A quartet maximum likelihood method for reconstructing tree topologies. Mol. Biol. Evol., 13:964-969, 1996.
26. K.M. Swenson, M. Marron, J.V. Earnest-DeYoung, and B.M.E. Moret. Approximating the true evolutionary distance between two genomes. In Proc. 7th SIAM Workshop on Algorithm Engineering & Experiments (ALENEX'05). SIAM Press, Philadelphia, 2005.
27. D.L. Swofford, G.J. Olsen, P.J. Waddell, and D.M. Hillis. Phylogenetic inference. In D.M. Hillis, B.K. Mable, and C. Moritz, editors, Molecular Systematics, pp. 407-514. Sinauer Assoc., Sunderland, MA, 1996.
28. J. Tang and B.M.E. Moret. Linear programming for phylogenetic reconstruction based on gene rearrangements. In Proc. 16th Ann. Symp. Combin. Pattern Matching (CPM'05), Lecture Notes in Computer Science, 2005.
29. J. Tang and B.M.E. 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, pp. i305-i312. Oxford U. Press, 2003.
30. J. Tang, B.M.E. Moret, L. Cui, and C.W. dePamphilis. Phylogenetic reconstruction from arbitrary gene-order data. In Proc. 4th IEEE Symp. on Bioinformatics and Bioengineering BIBE'04, pp. 592-599. IEEE Press, Piscataway, NJ, 2004.
31. L.-S. Wang, R.K. Jansen, B.M.E. Moret, L.A. Raubeson, and T. Warnow. Fast phylogenetic methods for genome rearrangement evolution: An empirical study. In Proc. 7th Pacific Symp. on Biocomputing (PSB'02), pp. 524-535. World Scientific Pub., 2002.
32. T. Warnow, B.M.E. Moret, and K. St. John. Absolute convergence: true trees from short sequences. In Proc. 12th Ann. ACM/SIAM Symp. Discrete Algs. (SODA'01), pp. 186-195. SIAM Press, 2001.