A method for reconstructing at least one phased chromosomal haplotype of at least one genomic segment of an ancestral couple of interest, the method comprising receiving, by a computer, genetic data for a plurality of individuals; analyzing, by the computer, the genetic data to identify a genomic DNA segment that is identical by descent among pairs of the individuals, the IBD genomic DNA segment identified by chromosome number and start and end coordinates, thereby identifying a set of pairs of individuals each pair sharing at least one IBD genomic DNA segment; receiving, by the computer, pedigree data for the set; analyzing, by the computer, the pedigree data to identify a most recent common ancestor (MRCA) of the set, the MRCA belonging to the ancestral couple; for each IBD genomic DNA segment shared by each pair of individuals, comparing, by the computer, phased haplotypes of each pair of individuals to determine an inferred IBD haplotype and to generate a plurality of inferred IBD haplotypes for the set of pairs of individuals, wherein generating the inferred IBD haplotype of one of the pairs of the individuals comprises for each inferred nucleotide letter of the inferred IBD haplotype, (i) responsive to the position of the inferred nucleotide letter in the DNA segment shared by the pair of individuals being heterozygous for one of the pair of individuals, or homozygous for the pair of individuals designating the position as unambiguous, (ii) responsive to the position of the inferred nucleotide letter in the DNA segment shared by the pair of individuals being heterozygous for the pair of individuals, designating the position as ambiguous; stitching together the inferred IBD haplotypes, by the computer, to generate stitched ancestral haplotypes reconstructing the phased chromosomal haplotypes of at least one genomic segment of the ancestral couple of interest, wherein stitching together the inferred IBD haplotypes comprises: ordering the inferred IBD haplotypes into an ordered set of IBD haplotypes; dividing the ordered set of IDB haplotypes into one or more groups by matching each inferred IBD haplotype with the group of the previous inferred haplotype of the ordered set based at least on a partial sequence identity that allows mismatches of nucleotide letters at one or more positions that are designated as ambiguous. receiving, by a computer, genetic data for a plurality of individuals; analyzing, by the computer, the genetic data to identify a genomic DNA segment that is identical by descent among pairs of the individuals, the IBD genomic DNA segment identified by chromosome number and start and end coordinates, thereby identifying a set of pairs of individuals each pair sharing at least one IBD genomic DNA segment; receiving, by the computer, pedigree data for the set; analyzing, by the computer, the pedigree data to identify a most recent common ancestor (MRCA) of the set, the MRCA belonging to the ancestral couple; for each IBD genomic DNA segment shared by each pair of individuals, comparing, by the computer, phased haplotypes of each pair of individuals to determine an inferred IBD haplotype and to generate a plurality of inferred IBD haplotypes for the set of pairs of individuals, wherein generating the inferred IBD haplotype of one of the pairs of the individuals comprises for each inferred nucleotide letter of the inferred IBD haplotype, (i) responsive to the position of the inferred nucleotide letter in the DNA segment shared by the pair of individuals being heterozygous for one of the pair of individuals, or homozygous for the pair of individuals designating the position as unambiguous, (ii) responsive to the position of the inferred nucleotide letter in the DNA segment shared by the pair of individuals being heterozygous for the pair of individuals, designating the position as ambiguous; (i) responsive to the position of the inferred nucleotide letter in the DNA segment shared by the pair of individuals being heterozygous for one of the pair of individuals, or homozygous for the pair of individuals designating the position as unambiguous, (ii) responsive to the position of the inferred nucleotide letter in the DNA segment shared by the pair of individuals being heterozygous for the pair of individuals, designating the position as ambiguous; stitching together the inferred IBD haplotypes, by the computer, to generate stitched ancestral haplotypes reconstructing the phased chromosomal haplotypes of at least one genomic segment of the ancestral couple of interest, wherein stitching together the inferred IBD haplotypes comprises: ordering the inferred IBD haplotypes into an ordered set of IBD haplotypes; dividing the ordered set of IDB haplotypes into one or more groups by matching each inferred IBD haplotype with the group of the previous inferred haplotype of the ordered set based at least on a partial sequence identity that allows mismatches of nucleotide letters at one or more positions that are designated as ambiguous. ordering the inferred IBD haplotypes into an ordered set of IBD haplotypes; dividing the ordered set of IDB haplotypes into one or more groups by matching each inferred IBD haplotype with the group of the previous inferred haplotype of the ordered set based at least on a partial sequence identity that allows mismatches of nucleotide letters at one or more positions that are designated as ambiguous.