A computer-implemented method for performing haplotype phasing, the computer-implemented method comprising: receiving a target individual genotype dataset of a target individual and a plurality of additional individual genotype datasets; generating a plurality of sub-cluster pairs of first parental groups and second parental groups, including for at least one of the sub-cluster pairs, classifying matched segments of the plurality of additional individual datasets into one of a first parental group of the sub-cluster pair and a second parental group of the sub cluster pair, such that the first parental group comprises a first set of matched segments selected from the plurality of additional individual datasets and the second parental group comprises a second set of matched segments selected from the plurality of additional individual datasets, said classifying comprising: identifying a plurality of informative sites, an informative site being a site with heterozygous allele values in the target individual genotype dataset and a homozygous allele value in an additional individual genotype dataset, identifying a conflicting informative site, the conflicting informative site being an informative site where two or more conflicting additional individual genotype datasets have contradicting homozygous alleles at the conflicting informative site, breaking at least one of the conflicting additional individual genotype datasets into two or more candidate matched segments, and classifying one or more of the candidate matched segments into one of the first parental group of the sub-cluster pair and the second parental group of the sub-cluster pair; linking the first parental groups and the second parental groups across the plurality of sub-cluster pairs to generate at least one super-cluster of a parental side; and performing haplotype phasing of the target individual based on the at least one the super-cluster. receiving a target individual genotype dataset of a target individual and a plurality of additional individual genotype datasets; generating a plurality of sub-cluster pairs of first parental groups and second parental groups, including for at least one of the sub-cluster pairs, classifying matched segments of the plurality of additional individual datasets into one of a first parental group of the sub-cluster pair and a second parental group of the sub cluster pair, such that the first parental group comprises a first set of matched segments selected from the plurality of additional individual datasets and the second parental group comprises a second set of matched segments selected from the plurality of additional individual datasets, said classifying comprising: identifying a plurality of informative sites, an informative site being a site with heterozygous allele values in the target individual genotype dataset and a homozygous allele value in an additional individual genotype dataset, identifying a conflicting informative site, the conflicting informative site being an informative site where two or more conflicting additional individual genotype datasets have contradicting homozygous alleles at the conflicting informative site, breaking at least one of the conflicting additional individual genotype datasets into two or more candidate matched segments, and classifying one or more of the candidate matched segments into one of the first parental group of the sub-cluster pair and the second parental group of the sub-cluster pair; identifying a plurality of informative sites, an informative site being a site with heterozygous allele values in the target individual genotype dataset and a homozygous allele value in an additional individual genotype dataset, identifying a conflicting informative site, the conflicting informative site being an informative site where two or more conflicting additional individual genotype datasets have contradicting homozygous alleles at the conflicting informative site, breaking at least one of the conflicting additional individual genotype datasets into two or more candidate matched segments, and classifying one or more of the candidate matched segments into one of the first parental group of the sub-cluster pair and the second parental group of the sub-cluster pair; linking the first parental groups and the second parental groups across the plurality of sub-cluster pairs to generate at least one super-cluster of a parental side; and performing haplotype phasing of the target individual based on the at least one the super-cluster.