POPGENE Software for Population Genetic Analysis

Molecular genetic markers (RAPD, SSR, RFLP, AFLP) 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 and animal breeders who are interested in population genetic properties of the 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 features of POPGENE, a popular program that can accommodate a variety of molecular marker types and perform many different types of analyses. It is important to note that you can obtain a free downloadable version of POPGENE from their website. The current version of POPGENE is designed specifically for the analysis of co-dominant and dominant markers using haploid and diploid data. It performs most types of data analysis encountered in population genetics and related fields. It can be used to compute summary statistics, including:
Allele Frequency: estimates gene frequencies at each locus from raw data.
Allele Number: counts the number of alleles with nonzero frequency.
Effective Allele Number: estimates the reciprocal of homozygosity.
Polymorphic Loci: percentage of all loci that are polymorphic regardless of allele frequencies.
Obs. Homozygosity: estimates proportion of observed homozygotes at a given locus.
Exp. Homozygosity: estimates proportion of expected homozygotes under random mating.
Shannon Index: estimates Shannon’s (1949) information index as a measure of gene diversity.
Gene Diversity: estimates Nei’s (1973) gene diversity.
Homogeneity Test: constructs two-way contingency tables and carries out chi-square and likelihood ratio (G 2) tests for homogeneity of gene frequencies across populations.
F-Statistics: estimates F-statistics (F_IT, F_ST and F_IS) (Hartl and Clark 1989).
Gene Flow: estimates gene flow from the estimate of GST or FST (Slatkin and Barton 1989).
Neutrality Test: performs the Ewens-Watterson test for neutrality using the algorithm given in Manly (1985).
Genetic Distance: estimates Nei’s (1972) genetic identity and genetic distance and Nei’s (1978) unbiased genetic identity and genetic distance.
Dendrogram: draws a text based dendrogram of Nei’s genetic distances evaluated by unweighed pair group method using arithmetic averages (UPGMA).

Popgene is a collection of simulations commonly used in the study of population genetics, including:
Hardy-Weinberg Equilibrium
Multiple Allele Inheritance
Multiple Loci Inheritance
Natural Selection
Genetic Drift
Migration
Mutation
Inbreeding

A three part screen allows users to simultaneously view the simulation parameters, data plots and a dynamic graph of the results. Parameter values, the speed of the simulation, and the scale size of the graph and the graph type can be easily changed. The operation of POPGENE is simple and straightforward. Select a simulation and graph type, then start it using the default parameters or those you enter from the keyboard. The outcome is shown in the results window and on the graph. Simulation parameters are easily changed, and the results may be saved to disk or printed. The package includes a step-by-step tutorial of the Hardy-Weinberg simulation, mini-tutorials using the other models, and suggested exercises to be used in conjunction with the simulations.