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REVIEW & INTERPRETATION

Software for Population Genetic Analyses of Molecular Marker Data

Institute for Genomic Diversity, Cornell Univ., Ithaca, NY 14853 USA

jl265{at}cornell.edu

ABSTRACT

Molecular genetic markers can be used to examine a group of individuals or populations to estimate various diversity measures and genetic distances, infer population structure and clustering patterns, test for Hardy-Weinberg and multilocus equilibrium, and test polymorphic loci for evidence of selective neutrality. This can be useful to plant breeders, germplasm managers, or others who are interested in population genetic properties of materials that they are working with. Many software programs for molecular population genetics studies have been developed for personal computers. Their easy access, implementation of sophisticated and powerful statistical techniques, and user-friendliness make them an attractive alternative to performing calculations on spreadsheets or by writing simpler programs for oneself. This review outlines the current major features of six popular programs (TFPGA, Arlequin, GDA, GENEPOP, GeneStrut, and POPGENE), including the types of data they handle, analyses they perform, and where they can be obtained (Table 1) . These particular programs were chosen because each can accommodate a variety of molecular marker types and perform many different types of analyses. Although there is much overlap in their functionality, each program has unique features to offer potential users.

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