function InitializeDistances (dummy)
{
	summingVector = {20,1}["1"];
	tracingVector = {20,20}["_MATRIX_ELEMENT_ROW_ == _MATRIX_ELEMENT_COLUMN_"];
	return 0;
}

function ComputeDistanceFormula (s1,s2)
{
	GetDataInfo (siteDifferenceCount, filteredData, s1, s2, DISTANCE_AMBIG_OPTION);
	totalDifference    = Transpose(summingVector)*(siteDifferenceCount$tracingVector*summingVector);
	totalSitesCompared = Transpose(summingVector)*(siteDifferenceCount*summingVector);
	totalDifference = totalDifference[0]/totalSitesCompared[0];
	totalDifference = 1-totalDifference-totalDifference^2/5;
	if (totalDifference<=0.0)
	{
		return 10;
	}
	return -Log(totalDifference);
}
