The Community for Technology Leaders
RSS Icon
Subscribe
Issue No.04 - October-December (2008 vol.5)
pp: 618-629
ABSTRACT
The incomplete perfect phylogeny (IPP) problem and the incomplete perfect phylogeny haplotyping (IPPH) problem deal with constructing a phylogeny for a given set of haplotypes or genotypes with missing entries. The earlier approaches for both of these problems dealt with restricted versions of the problems, where the root is either available or can be trivially re-constructed from the data, or certain assumptions were made about the data. In this paper, we deal with the unrestricted versions of the problems, where the root of the phylogeny is neither available nor trivially recoverable from the data. Both IPP and IPPH problems have previously been proven to be NPcomplete. Here, we present efficient enumerative algorithms that can handle practical instances of the problem. Empirical analysis on simulated data shows that the algorithms perform very well both in terms of speed and in terms accuracy of the recovered data.
INDEX TERMS
Phylogenetics, Perfect Phylogeny, Incomplete Perfect Phylogeny, Haplotype Inference
CITATION
Ravi Vijaya Satya, Amar Mukherjee, "The Undirected Incomplete Perfect Phylogeny Problem", IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.5, no. 4, pp. 618-629, October-December 2008, doi:10.1109/TCBB.2007.70218
REFERENCES
[1] R. Agarwala and D. Fernandez-Baca, “A Polynomial-Time Algorithm for the Perfect Phylogeny Problem When the Number of Character States Is Fixed,” SIAM J. Computing, vol. 23, pp. 1216-1224, 1994.
[2] HapMapConsortium, “The International Hapmap Project,” Nature, vol. 426, pp. 789-796, Dec. 2003.
[3] A.G. Clark, “Inference of Haplotypes from PCR-Amplified Samples of Diploid Populations,” Molecular Biology and Evolution, vol. 7, pp. 111-122, 1990.
[4] D. Gusfield, “Haplotyping as Perfect Phylogeny: Conceptual Framework and Efficient Solutions,” Proc. Ann. Int'l Conf. Research in Computational Molecular Biology (RECOMB), 2002.
[5] Y. Liu and C.-Q. Zhang, “A Linear Solution for Haplotype Perfect Phylogeny Problem,” Proc. Int'l Conf. Bioinformatics and Its Applications (ICBA), 2004.
[6] R. Vijaya Satya and A. Mukherjee, “An Efficient Algorithm for Perfect Phylogeny Haplotyping,” Proc. IEEE CS Computational Systems Bioinformatics Conf. (CSB '05), pp. 103-110, Aug. 2005.
[7] Z. Ding, V. Filkov, and D. Gusfield, “A Linear Time Algorithm for the Perfect Phylogeny Haplotyping (PPH) Problem,” Proc. Ann. Int'l Conf. Research in Computational Molecular Biology (RECOMB '05), pp. 585-600, 2005.
[8] Z. Ding, V. Filkov, and D. Gusfield, “A Linear Time Algorithm for the Perfect Phylogeny Haplotyping (PPH) Problem,” J. Computational Biology, vol. 13, no. 2, pp. 522-553, 2006.
[9] R. Vijaya Satya and A. Mukherjee, “An Optimal Algorithm for Perfect Phylogeny Haplotyping,” J. Computational Biology, vol. 13, no. 4, pp. 897-928, 2006.
[10] M. Steel, “The Complexity of Reconstructing Trees from Qualitative Characters and Subtrees,” J. Classification, vol. 9, pp. 91-116, 1992.
[11] I. Peer, T. Pupko, R. Shamir, and R. Sharan, “Incomplete Directed Perfect Phylogeny,” SIAM J. Computing, vol. 33, no. 3, pp. 590-607, 2004.
[12] G. Kimmel and R. Shamir, “The Incomplete Perfect Phylogeny Problem,” J. Bioinformatics and Computational Biology, vol. 3, no. 2, pp. 1-25, 2005.
[13] E. Halperin and R. Karp, “Perfect Phylogeny and Haplotype Assignment,” Proc. Ann. Int'l Conf. Research in Computational Molecular Biology (RECOMB), 2004.
[14] R. Vijaya Satya and A. Mukherjee, The Undirected Incomplete Perfect Phylogeny Problem, Technical Report CS-TR-05-11, School of Computer Science, Univ. of Central Florida, Dec. 2005.
[15] J. Gramm, T. Nierhoff, R. Sharan, and T. Tantau, “Haplotyping with Missing Data via Perfect Path Phylogenies,” Proc. Second RECOMB Satellite Workshop Computational Methods for SNPs and Haplotypes, pp. 35-46, 2004.
[16] V. Bafna, D. Gusfield, G. Lancia, and S. Yooseph, “Haplotyping as Perfect Phylogeny: A Direct Approach,” J. Computational Biology, vol. 10, nos. 3-4, pp. 323-340, 2003.
[17] R. Hudson, “Generating Samples under the Wright-Fisher Neutral Model of Genetic Variation,” Bioinformatics, vol. 18, pp. 337-338, 2002.
23 ms
(Ver 2.0)

Marketing Automation Platform Marketing Automation Tool