Typical applications are malaria parasites associated with drug resistance, where loci correspond to specific codons in one or more genes, e.g., codons 51, 59, 108, 164 in the dhfr locus and codons 436, 437, 540, 581, 613 in the dhps locus of P. falciparum associated with resistance to sulfadoxine-pyrimethamine (SP). Here, DHPS is linked to malaria.