The two copies are highly similar to each other. A haplotype is the sequence of nucleotides in a chromosome. the haplotype phasing problem is focused on the nucleotides where the two homologous chromosomes differ. Computationally, for a genomic region with K differing nucleotide sites, there are 2^K - 1 possible haplotypes, so the phasing problem focuses on efficiently finding the most probable haplotypes given an observed genotype.