Table 5.

Index of similarity (I_F) between haplotype frequencies estimated with and without molecular haplotyping information.

	PL-EM	PHASE
258 Spanish [45]	0.996	0.996
137 Nicaraguans [30]	0.986	0.986
112 UK Caucasians [24]	0.994	0.998
101 Black South Africans [24]	0.981	0.988
1000 Koreans [31]	0.997	0.998

Computations of I_F indices were based on the haplotype frequency estimates obtained by considering all possible haplotype configurations (with a nonzero probability) inferred for each subject, weighted by their estimated probability. Note that such estimates can be rather different from those obtained by gene counting on the basis of the "best" reconstruction (that is, when only the most probable pair of haplotype is selected for each sampled individual). Since Haplotyper only provides a summary of the frequency with which each haplotype occurred in the "best" reconstruction, it was excluded from the comparison.