the present invention relates to a method , system and software arrangement for determining the co - associations of allele types across consecutive loci and hence for reconstructing two haplotypes of a diploid individual from genotype data generated by mapping experiments with single molecules , families or populations . the haplotype reconstruction system , method and software arrangement of the present invention can utilize a procedure that is nearly linear in the number of polymorphic markers examined , and is therefore quicker , more accurate , and more efficient than other population - based approaches . the system , method , and software arrangement of the present invention may be useful to assist with the diagnosis and treatment of any disease , which has a genetic component .