Figure 1

A pair-wise alignment ( S^A, S^B) is shown for sequences A = agtggaaa and B = acggcca. A recombination $S^{A^{\prime }}$ and $S^{B^{\prime }}$ is obtained by interchanging the shaded areas. The corresponding bitvector is I = 0110000. A pair-wise alignment (S^X, S^Y) is shown for sequences X = acggaaa and Y = agtggcca. The pair of haploids to diploid distance between (S^A, S^B) and (X, Y) is 0 + 1 = 1, and is obtained using the recombination $\left(S^{A^{\prime }},S^{B^{\prime }}\right)$ and unit cost edit distance as the measure. The plain unit cost edit distance between (A, B) and (X, Y) is 2 + 3 = 5. The plain unit cost edit distance between (A, B) and (Y, X) is 3 + 2 = 5. The synchronized diploid to diploid distance between (S^A, S^B) and (S^X, S^Y) is 3, using unit cost edit distance as the measure.