Identifying Long Haplotype Blocks with Low Diversity

Given an m×n haplotype matrix A, we show linear time algorithms for finding all interval diversities, farthest sites, and the longest block with low diversity. For selecting the multiple long blocks with diversity constraint, we show that selecting k blocks with longest total length can be be found in O(nk). We also propose linear time algorithms in calculating the all intra-longest-blocks and all intra-k-longestblocks. For dealing with missing SNP data, we propose methods that clarifies ambiguous SNP sites; furthermore, we show some hardness result concerning the minimum di-