1function InitializeDistances (dummy)
2{
3	summingVector = {4,1}["1"];
4	return 0;
5}
6
7function ComputeDistanceFormula (s1,s2)
8{
9	GetDataInfo (siteDifferenceCount, filteredData, s1, s2, RESOLVE_AMBIGUITIES);
10	totalSitesCompared = (Transpose(summingVector)*(siteDifferenceCount*summingVector))[0];
11	if (totalSitesCompared)
12	{
13		return 1-(siteDifferenceCount[0][0]+siteDifferenceCount[1][1]+siteDifferenceCount[2][2]+siteDifferenceCount[3][3])/totalSitesCompared;
14	}
15	return 1000;
16}
17