Reconciliation problems for duplication, loss and horizontal gene transfer

Proceedings of the Annual International Conference on Computational Molecular Biology, RECOMB

Volumn 8, Issue , 2004, Pages 316-325

  Górecki, Paweł ^a  

^a UNIVERSITY OF WARSAW   (Poland)

Author keywords

Duplication loss model; Horizontal gene transfer; NP completeness; Reconciliation

Indexed keywords

ALGORITHMS; COMPUTATIONAL METHODS; DATABASE SYSTEMS; GENETIC ENGINEERING; POLYNOMIALS; PROBLEM SOLVING; RANDOM PROCESSES; TREES (MATHEMATICS);

DUPLICATION-LOSS MODEL; HORIZONTAL GENE TRANSFER; NP-COMPLETENESS; RECONCILIATION;

GENES;

EID: 2442593866     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1145/974614.974656     Document Type: Conference Paper

References (14)

1. M. A. Charleston. Jungles: A new solution to the host/parasite phylogeny reconciliation problem. Mathematical Bioaciences, 149:191-223, 1998.
2. W. Doolittle. Phylogenetic classification and the universal tree. Science, 284:2124-9, 2000.
3. O. Eulenstein, B. Mirkin, and M. Vingron. Duplication-based measures of difference between gene and species trees. Journal of Computational Biology, 1:135-148, 1998.
4. M. R. Garey and D. S. Johnson. Computers and Intractability: A Guide to NP-Completeness. W.H. Freeman and Company, San Francisco, California. 1979.
5. M. Goodman, J. Czelusniak, G. W. Moore, A. E. Romero-Harrera, and G. Matsuda. Fitting the gene lineage into its species lineage. A parsimony strategy illustrated by cladograms constructed from globin sequences. Syst. Zool., 28:132-163, 1979.
6. M. T. Hallett and J. Lagergren. New algorithms for the duplication-loss model. In R. Shamir, S. Miyano, S. Istrail, P. Pevzner, and M. Waterman, editors, Proceedings of the 4th Annual International Conference on Computational Molecular Biology (RECOMB-00), pages 138-146, N.Y., Apr. 8-11 2000. ACM Press.
7. M. T. Hallett and J. Lagergren. Efficient algorithms for lateral gene transfer problems. In T. Lengauer, D. Sankoff, S. Istrail, P. Pevzner, and M. Waterman, editors, Proceedings of the Fith International Conference on Computational Biology (RECOMB-01), pages 149-156, New York, Apr. 22-25 2001. ACMPress.
8. B. Ma, M. Li, and L. Zhang. On Reconstructing Species Trees from Gene Trees in Term of Duplications and Losses. In RECOMB 1998, pages 182-191, 1998.
9. B. Mirkin, I. Muchnik, and T. F. Smith. A biologically meaningful model for comparing molecular phytogenies. Technical Report 95-28, DIMACS, Aug. 9 1995.
10. R. D. M. Page. Maps between trees and cladistic analysis of historical associations among genes, organisms, and areas. Systematic Biology, 43:58-77, 1994.
11. H. Philippe and P. Forterre. The rooting of the universal tree of life is not reliable. Journal of Molecular Evolution, 49:509-523, 1999.
12. R. D. M. Page. Component analysis: A valiant failure? Cladistics, 6:119-36, 1990.
13. M. Steel. The complexity of reconstructing trees from qualitative characters and subtrees. J. Classification, 9:91-116, 1992.
14. M. Syvanen and C. I. Kado. Horizontal Gene Transfer. Chapman & Hall, 2000.