Scilight Press

Numerous programs for studying population genetics using molecular data have been developed. The present study compared the features of such freely available softwares viz., STRUCTURE, Arlequin, PopGene, PowerMarker and Winboot. In this comparative study, the molecular data from 28 rice varieties at 42 loci obtained using simple sequence repeat markers were used. Even though the results produced by all the softwares were found to be in corollary, but there were marked differences in their attributes as analysis each software offered, its graphical interface, type of data it supported and method it was based on. The study demonstrated that among all the studied softwares, PowerMarker was best for analyzing genetic relationship using codominant genotypic data. STRUCTURE was best for finding genetic structure, whereas Arlequin was appropriate for haplotypic data. PopGene should be used only with closely related species represented by codominant data. Winboot should also be used with codominant data only.