Simultaneous identification of duplications and lateral transfers

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

Volumn 8, Issue , 2004, Pages 347-356

  Hallett, Mike ^a   Lagergren, Jens ^b   Tofigh, Ali ^b  

^a MCGILL UNIVERSITY   (Canada)

^b ROYAL INSTITUTE OF TECHNOLOGY   (Sweden)

Author keywords

Gene duplication; Gene loss; Lateral gene transfer

Indexed keywords

ALGORITHMS; COMPUTATIONAL METHODS; COMPUTER SIMULATION; DYNAMIC PROGRAMMING; GENES; MAPPING; PARAMETER ESTIMATION; PROBLEM SOLVING;

GENE DUPLICATION; GENE LOSS; LATERAL GENE TRANSFER; SPECIES TREES;

GENETIC ENGINEERING;

EID: 2442573762     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1145/974614.974660     Document Type: Conference Paper

References (19)

1. Addario-Berry, L., Hallett, M., Lagergen, J. (2003) Towards identifying lateral gene transfer events. Pacific symposium on bioinformatics (PSB '03), Hawaii, January, 132-141.
2. Arvestad, L, Berglund, A. C., Lagergren, J. and Sennblad, B. (2003) Bayesian gene/species tree reconciliation and orthology analysis using MCMC. Bioinformatics/ISMB '03, 19, i7-i15.
3. Charleston, M. A. (2000) Jungles: a new solution to the host/parasite phylogeny reconciliation problem. Math, Biosci..
4. th Annual ACM-SIAM Symposium on Discrete Algorithms, SODA '97, pp. 427-436.
5. DasGupta, B., He. X., Jiang, T., Li, M., Tromp, J. and Zhang, L. (1999) On the linear-cost subtree-transfer distance between phylogenetic trees. Algorithmica special issue on computational biology 25, pp. 176-195.
6. Goodman, M. et al. (1979) Fitting the Gene Lineage into its species lineage: a parsimony strategy illustrated by cladograms constructed from globin sequences. Syst. Zool, 28.
7. Guigó, R. et al. Reconstruction of ancient molecular phylogenies. Molec. Phylogenet, and Evol., 6, 2, pp. 189-213.
8. th Annual RECOMB '00, Tokyo, Japan, pp. 146-158.
9. th Annual RECOMB '01, Montreal, Canada, pp. 141-148.
10. Hallett, M. and Lagergren, J. (2004) Identifying Lateral Gene Transfer Events. Full journal version. Submitted to SIAM J. Comp.. Available at http://www.mcb.mcgill.ca/~hallett/Lateral.pdf.
11. Hein. J. (1990) Reconstructing the evolution of sequences subject to recombination using parsimony. Math. Biosci., 98, pp. 185-200.
12. Hein. J. (1993) A heuristic method to reconstruct the history of sequences subject to recombination. J. Mol. Evol., 36, pp. 396-405.
13. Hein, J., Jiang, T., Wang, L. and Zhang, K. (1996) On the complexity of comparing evolutionary trees. Discrete Applied Mathematics, 71, pp. 153-169.
14. Holmes, E. C., Worobey, M., and Rambaut, A. (1999) Phylogenetic evidence for recombination in Dengue virus. Mol. Biol. Evol., 16(3), pp. 405-409.
15. Lawerence, J. G. and Hart, D. L. (1992) Inference of horizontal genetic transfer: an approach using bootstrap. Genetics, 131, 753-760.
16. Ochman, H., Lawerence, J. G. and Groisman, E. A. (2000) The nature of bacterial innovation. Nature, 405, 299-307.
17. Page, R. D. M. (1994) Maps between trees and cladistic analysis of historical associations among genes, organisms and areas. Syst. Biol., 43. pp. 58-77.
18. Page, R. D. M. and Charleston, M. A. (1997) From gene to organismal phylogeny: Reconciled trees and the gene tree/species tree problem. Molecular Phylogenetics and Evolution, 7, pp. 231-240.
19. von Haseler, A. and Churchill, G. A. (1993) Network models for sequence evolution. J. Mol. Evol., 37, pp. 77-85.