Algorithms for Imperfect Phylogeny Haplotyping (IPPH) with a single homoplasy or recombination event

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 3692 LNBI, Issue , 2005, Pages 152-164

  Song, Yun S ^a   Wu, Yufeng ^a   Gusfield, Dan ^a  

^a University of California   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHMS; DATA REDUCTION; HEURISTIC METHODS; MATHEMATICAL MODELS; POLYNOMIAL APPROXIMATION; PROBLEM SOLVING;

HAPLOTYPE INFERENCE (HI); IMPERFECT PHYLOGENY HAPLOTYPING (IPPH); RECOMBINATION EVENT; SINGLE HOMOPLASY;

COMPUTER SCIENCE;

EID: 33646165723     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/11557067_13     Document Type: Conference Paper

References (21)

1. B. L. Allen and M. Steel. Subtree transfer operations and their induced metrics on evolutionary trees. Ann. Combin., 5:1-13, 2001.
2. V. Bafna, D. Gusfield, G. Lancia, and S. Yooseph. Haplotyping as perfect phylogeny: A direct approach. J. Comput. Biol., 10:323-340, 2003.
3. T. Barzuza, J.S. Beckman, R. Shamir, and I. Pe'er. Computational problems in perfect phylogeny haplotyping: XOR genotypes and tag SNPs. In Proc. of CPM, pages 14-31, 2004.
4. R.H. Chung and D. Gusfield. Empirical exploration of perfect phylogeny haplotyping and haplotypers. In Proc. of COCOON, pages 5-19, 2003.
5. International HapMap Consortium. The HapMap project. Nature, 426:789-796, 2003.
6. Z. Ding, V. Filkov, and D. Gusfield. A linear-time algorithm for the perfect phylogeny haplotyping problem. In Proc. of RECOMB, pages 585-600, 2005.
7. E. Eskin, E. Halperin, and R. Karp. Large scale reconstruction of haplotypes from genotype data. In Proc. of RECOMB, pages 104-113, 2003.
8. E. Eskin, E. Halperin, and R.M. Karp. Efficient reconstruction of haplotype structure via perfect phylogeny. J. Bioinf. Comput. Biol., 1:1-20, 2003.
9. D. Gusfield. Haplotyping as perfect phylogeny: Conceptual framework and efficient solutions (Extended Abstract). In Proc. of RECOMB, pages 166-175, 2002.
10. D. Gusfield. Optimal, efficient reconstruction of Root-Unknown phylogenetic networks with constrained recombination. J. Comput. Sys. Sci., 70:381-398, 2005.
11. D. Gusfield, S. Eddhu, and C. Langley. Optimal, efficient reconstruction of phylogenetic networks with constrained recombination. J. Bioinf. Comput. Biol., 2(1):173-213, 2004.
12. E. Halperin and E. Eskin. Haplotype reconstruction from genotype data using Imperfect Phylogeny. Bioinformatics, 20:1842-1849, 2004.
13. J. Hein. Reconstructing evolution of sequences subject to recombination using parsimony. Math. Biosci., 98:185-200, 1990.
14. R. Hudson. Gene genealogies and the coalescent process. Oxford Survey of Evolutionary Biology, 7:1-44, 1990.
15. R. Hudson. Generating samples under the Wright-Fisher neutral model of genetic variation. Bioinformatics, 18:337-338, 2002.
16. S. Lin, D.J. Cutler, M.E. Zwick, and A. Chakravarti. Haplotype inference in random population samples. Am. J. Hum. Genet., 71:1129-1137, 2002.
17. C. Semple and M. Steel. Phylogenetics. Oxford University Press, UK, 2003.
18. Y. S. Song. On the combinatorics of rooted binary phylogenetic trees. Ann. Combin., 7:365-379, 2003.
19. Y. S. Song and J. Hein. Constructing minimal ancestral recombination graphs. J. Comput. Biol., 12:147-169, 2005.
20. M. Stephens, N.J. Smith, and P. Donnelly. A new statistical method for haplotype reconstruction from population data. Am. J. Hum. Genet. 68:978-989, 2001.
21. S. Tavaré. Calibrating the clock: Using stochastic processes to measure the rate of evolution. In E. Lander and M. Waterman, editors, Calculating the Secrets of Life. National Academy Press, 1995.