Self-Optimizing Parallel Algorithms for Haplotype Reconstruction and Their Evaluation on the JPT and CHB Genotype Data

The haplotype reconstruction problem has received a great deal of attention in the bioinformatics literature. The algorithms proposed thus far for this problem can be grouped into two main categories: statistical and combinatorial. In this paper, we focus on combinatorial algorithms for haplotype reconstruction based on Clark´s method. Specifically, we propose several self-optimizing parallel algorithms for haplotype reconstruction based on Clark´s method. Experimental results show that the proposed self-optimizing parallel algorithms can be viewed as an efficient alternative not only to Clark´s algorithm, but also to some previously proposed (integer) linear programming formulations.