Phylogenetic reconstruction from arbitrary gene-order data

Proceedings - Fourth IEEE Symposium on Bioinformatics and Bioengineering, BIBE 2004

Volumn , Issue , 2004, Pages 592-599

  Tang, Jijun ^a   Moret, Bernard M E ^a   Cui, Liying ^b   DePamphilis, Claude W ^b  

^a University of New Mexico   (United States)

^b PENNSYLVANIA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGAE; BIOMARKERS; CELLS; COMPUTATIONAL COMPLEXITY; COMPUTER SIMULATION; DATA REDUCTION; DATABASE SYSTEMS; DNA;

GENE-ORDER DATA; PHYLOGENETIC RECONSTRUCTION; PLASTID GENOMES; TRANSPOSITIONS;

GENES;

EID: 4544340629     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (23)

1. D. Bader, B. Moret, J. Tang, and T. Warnow. GRAPPA (Genome Rearrangements Analysis under Parsimony and other Phylogenetic Algorithms). www.cs.unm.edu/~moret/GRAPPA/.
2. D. Bhattacharya, K. Weber, S. An, and W. Berning-Koch. Actin phylogeny identifies Mesostigma viride as a flagellate ancestor of the land plants. J. Mol. Evol., 47:544-550, 1998.
3. M. Blanchette, G. Bourque, and D. Sankoff. Breakpoint phylogenies. In S. Miyano and T. Takagi, editors, Genome Informatics, pages 25-34. Univ. Academy Press, Tokyo, 1997.
4. M. Blanchette, T. Kunisawa, and D. Sankoff. Gene order breakpoint evidence in animal mitochondrial phylogeny. J. Mol. Evol., 49:193-203, 1999.
5. A. Caprara. Formulations and hardness of multiple sorting by reversals. In Proceedings of the 3rd Int'l Conference on Comput. Mol. Biol. RECOMB99, pages 84-93. ACM Press, 1999.
6. A. Caprara. On the practical solution of the reversal median problem. In Proc. 1st Int'l Workshop Algorithms in Bioinformatics (WABI01), volume 2149 of Lecture Notes in Computer Science, pages 238-251. Springer-Verlag, 2001.
7. M. Cosner, R. Jansen, B. Moret, L. Raubeson, L.-S. 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: Empirical and Analytical Approaches to Gene Order Dynamics, Map Alignment, and the Evolution of Gene Families, pages 99-121. Kluwer Academic Pubs., Dordrecht, Netherlands, 2000.
8. S. Downie and J. Palmer. Use of chloroplast DNA rear-rangements in reconstructing plant phylogeny. In D. Soltis, P. Soltis, and J. Doyle, editors, Molecular Systematics of Plants, pages 14-35. Chapman and Hall, New York, 1992.
9. N. El-Mabrouk. Genome rearrangement by reversals and insertions/ deletions of contiguous sements. In Proc. 11th Ann. Symp. Combinatorial Pattern Matching (CPM'00), volume 1848 of Lecture Notes in Computer Science, pages 222-234, 2000.
10. K. Karol, R. McCourt, M. Cimino, and C. Delwiche. The closest living relatives of land plants. Science, 294:2351-2353, 2001.
11. C. Lemieux, C. Otis, and M. Tunnel. Ancestral chloroplast genome in Mesostigma viride reveals an early branch of green plant evolution. Nature, 403:649-652, 2000.
12. M. Marron, K. Swenson, and B. Moret. Genomic distances under deletions and insertions. In Proc. 9th Int'l Conf. Computing and Combinatorics (COCOON03), volume 2697 of Lecture Notes in Computer Science, pages 537-547. Springer-Verlag, 2003.
13. W. Martin, B. Stoebe, V. Goremykin, S. Hansmann, and M. Hasegawa. Gene transfer to the nucleus and the evolution of chloroplasts. Nature, 393:162-165, 1998.
14. J. Maul, J. Lilly, L. Cui, C. dePamphilis, W. Miller, E. Harris, and D. Stern. Chlamydomonas chloroplast chromosome: islands of genes in a sea of repeats. Plant Cell, 14:2659-2679, 2002.
15. A. McLysaght, P. Baldi, and B. Gaut. Extensive gene gain associated with adaptive evolution of poxviruses. Proc. Nat'l Acad. Sci., USA, 100:15655-15660, 2003.
16. B. Moret, J. Tang, L.-S. Wang, and T. Warnow. Steps toward accurate reconstruction of phylogenies from gene-order data. J. Comput. Syst. Sci., 65(3):508-525, 2003.
17. B. Moret, L.-S. Wang, T. Warnow, and S. K. Wyman. New approaches for reconstructing phylogenies from gene-order data. In Proc. 9th Int'l Conf. on Intelligent Systems for Molecular Biology (ISMB01), volume 17 of Bioinformatics, pages S165-S173. Oxford U. Press, 2001.
18. B. Moret, S. K. Wyman, D. A. Bader, T. Warnow, and M. Yan. A new implementation and detailed study of break-point analysis. In Proc. 6th Pacific Symp. on Biocomputing (PSB01), pages 583-594. World Scientific Pub., 2001.
19. D. Sankoff and M. Blanchette. Multiple genome rearrangement and breakpoint phylogeny. J. Comput. Biol., 5:555-570, 1998.
20. A. Siepel and B. Moret. Finding an optimal inversion median: experimental results. In Proc. 1st Int'l Workshop Algorithms in Bioinformatics (WABI01), volume 2149 of Lecture Notes in Computer Science, pages 189-203. Springer-Verlag, 2001.
21. J. Tang and B. Moret. Phylogenetic reconstruction from gene rearrangement data with unequal gene contents. In Proc. 8th Workshop on Algorithms and Data Structures (WADS03), volume 2748 of Lecture Notes in Computer Science, pages 37-46. Springer-Verlag, 2003.
22. J. Tang and B. Moret. Scaling up accurate phylogenetic reconstruction from gene-order data. In Proc. 11th Int'l Conf. on Intelligent Systems for Molecular Biology (ISMB03), volume 19 of Bioinformatics, pages i305-i312. Oxford U. Press, 2003.
23. K. Wolfe, C. Morden, and J. Palmer. Function and evolution of a minimal plastid genome from a nonphotosynthetic parasitic plant. Proc.. Nat'l Acad. Sci., USA, 89:10648-10652, 1992.