def count(self,sequence1,sequence2):
dec1 = FrequenceAnalysis.FrequenceAnalysis(sequence1)
dec2 = FrequenceAnalysis.FrequenceAnalysis(sequence2)
'''
probability no substitution occurs
'''
#sites_count = len(min([dec1,dec2], key = len))
sites_count = len(dec1)
different_sites = 0
for e1,e2 in zip(dec1,dec2):
different_sites += (1- Model.dotProduct(e1,e2))
#return (-float(3)/4)* log1p(-(float(4)/3)*different_sites/sites_count)
return different_sites/sites_count
