An EM method based on entropy LD block partition for haplotype inference

Genetic diseases have attracted much attention to the genetic research which depends on the data named haplotypes. Because of most haplotypes are generated from genotypes, haplotype inference (HI) problem becomes very popular. To solve this problem, we propose a new method based on EM and partition-ligation (PL) strategy. Compared to the previous methods, our algorithm uses the PL strategy based on multilocus linkage disequilibrium (LD), which has an advantage over the uniform block partition and pairwise LD. Considering the scale of data and the missing alleles, we also change the ligation strategy to control the complexity of time and space. The experimental results on the real data and the simulated data show that the algorithm in this paper has better performance than previous ones.