Haplotyping as Perfect Phylogeny

For diploid organisms (e.g. humans), each chromosome is present in two non-exact copies and the description of all the data from a single chromosome is called a haplotype. Obtaining haplotype data is important in applications such as analyzing complex diseases, however this is a very difficult problem to solve experimentally and finding mixed genotype data is much less technically difficult and cost effective. So, while we can determine that at a specific site (if we call the two states, or alleles this state can occupy 0 and 1), an individual may have either two 0’s, two 1’s or one 0 and one 1, in the last case, distinguishing which state comes from which chromosome is very hard to discern experimentally. Therefore, we have the problem that experimentally, we may not be able to distinguish between the case where the haplotype of an individual is either of the below pairs: {( 0 0 )