DISTANCES BETWEEN HAPLOTYPES

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We are interested in the genetic distance between pairs of haplotypes.

Let Xj be a Boolean vector, of length S, representing the jth haplotype.
S is the number of restriction sites or marker bands.

The squared distance between haplotypes hj and hk is:

distance

The total sum of squares of the distances between all pairs of haplotypes is equivalent to the conventional sum of squares of deviations of multidimensional vectors from the centroid of a multidimensional space.

The analysis of molecular variance is essentially an analysis of variance using squared distances between pairs of haplotypes as the data.

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