Computational Methods for SNPs and Haplotype Inference: by Andrew G. Clark, Emmanouil T. Dermitzakis, Stylianos E.

By Andrew G. Clark, Emmanouil T. Dermitzakis, Stylianos E. Antonarakis (auth.), Sorin Istrail, Michael Waterman, Andrew Clark (eds.)

This publication constitutes the post-proceedings of the DIMACS/RECOMB satellite tv for pc Workshop on Computational tools for SNPs and Haplotype Inference held in Piscataway, NJ, united states, in November 2002.

The booklet offers ten revised complete papers in addition to abstracts of the remainder workshop papers. All suitable present matters in computational tools for SNP and haplotype research and their purposes to disorder institutions are addressed.

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Extra info for Computational Methods for SNPs and Haplotype Inference: DIMACS/RECOMB Satellite Workshop, Piscataway, NJ, USA, November 21-22, 2002. Revised Papers

Example text

3 Clark’s Rule and Population Models The observation that the maximum likelihood method could be modeled by a certain probabilistic application of Clark’s rule was known to researchers, Stephens, Smith, and Donnelly [50], who proposed a modification of the ML sampling procedure of the previous section. Their modification introduces an approximate population genetics model [48] as a prior for observing the set of haplotypes. Instead of phasing randomly selected individuals with probabilities weighted by φh φh¯ , they proposed a more complicated probability rule, where the weight ¯ for g is given by of phasing h, h g ¯ δh+ ¯ (h\h\h) ¯ πh (h\h) · πh h (3) where h\h is the sequence of haplotypes h with one occurrence of h removed.

D. J. Schork. Accuracy of haplotype frequency estimation for biallelic loci, via the expectation-maximization algorithm for unphased diploid genotype data. American Journal of Human Genetics, 67(4):947–59, 2000. 17. L. Frisse, R. Hudson, A. Bartoszewicz, J. Wall, T. Donfalk, and A. Di Rienzo. Gene conversion and different population histories may explain the contrast between polymorphism and linkage disequilibrium levels. American Journal of Human Genetics, 69:831–843, 2001. 18. Gideon Greenspan and Dan Geiger.

The fine structure of galls in phylogenetic networks with recombination. Technical report, UC Davis, Department of Computer Science, 2003. 23. L. Helmuth. 0. Science, 293(5530):583–585, 2001. 24. E. Hubbel. Personal Communication, August 2000. 25. R. Hudson. Gene genealogies and the coalescent process. Oxford Survey of Evolutionary Biology, 7:1–44, 1990. 26. G. Lancia, C. Pinotti, and R. Rizzi. Haplotyping populations: Complexity and approximations, technical report dit-02-082. Technical report, University of Trento, 2002.

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