An almost linear-time algorithm for graph realization
Mathematics of Operations Research
Algorithms on strings, trees, and sequences: computer science and computational biology
Algorithms on strings, trees, and sequences: computer science and computational biology
Haplotyping as perfect phylogeny: conceptual framework and efficient solutions
Proceedings of the sixth annual international conference on Computational biology
Efficient Reconstruction of Haplotype Structure via Perfect Phylogeny
Efficient Reconstruction of Haplotype Structure via Perfect Phylogeny
Haplotyping with missing data via perfect path phylogenies
Discrete Applied Mathematics
On the complexity of SNP block partitioning under the perfect phylogeny model
WABI'06 Proceedings of the 6th international conference on Algorithms in Bioinformatics
Algorithms for imperfect phylogeny haplotyping (IPPH) with a single homoplasy or recombination event
WABI'05 Proceedings of the 5th International conference on Algorithms in Bioinformatics
A linear-time algorithm for the perfect phylogeny haplotyping (PPH) problem
RECOMB'05 Proceedings of the 9th Annual international conference on Research in Computational Molecular Biology
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The next high-priority phase of human genomics will involve the development of a full Haplotype Map of the human genome [15]. It will be used in large-scale screens of populations to associate specific haplotypes with specific complex genetic-influenced diseases. A key, perhaps bottleneck, problem is to computationally determine haplotype pairs from genotype data. An approach to this problem based on viewing it in the context of perfect phylogeny was introduced in [14] along with an efficient solution. A slower (in worst case) variation of that method was implemented [3]. Two simpler methods for the perfect phylogeny approach that are also slower (in worst case) than the first algorithm were later developed [1,7]. We have implemented and tested all three of these approachs in order to compare and explain the practical efficiencies of the three methods. We discuss two other empirical observations: a strong phase-transition in the frequency of obtaining a unique solution as a function of the number of individuals in the input; and results of using the method to find non-overlapping intervals where the haplotyping solution is highly reliable, as a function of the level of recombination in the data. Finally, we discuss the biological basis for the size of these tests.