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POPGENE is a joint project development by Francis Yeh , Rongcai Yang and Timothy Boyle. It is a user-friendly computer freeware for the analysis of genetic variation among and within populations using co-dominant and dominant markers. This package provides the Windows graphical user interface that makes population genetics analysis more accessible for the casual computer user and more convenient for the experienced computer user. Simple menus and dialog box selections enable you to perform complex analyses and produce scientifically sound statistics, thereby assisting you to adequately analyze population genetic structure using the target markers.

PC users can run POPGENE under Microsoft® Windows 3.11, 95, 98, 2000, ME and NT.

APPLE users can run POPGENE on PowerPc, G3 and G4. However, they must first install a software such as "Virtual PC" or “Soft Windows” . The 16- and 32-bit version of POPGENE would ran effortlessly.

The current version (Version 1.32) is designed specifically for the analysis of co-dominant and dominant markers using haploid and diploid data. POPGENE computes both comprehensive genetic statistics (e.g., allele frequency, gene diversity, genetic distance, G-statistics, F-statistics) and complex genetic statistics (e.g., gene flow, neutrality tests, linkage disequilibria, multi-locus structure). The development of a new version to include the analysis of quantitative genetic variation and covariation and the comparison of marker genes and quantitative genetic variation is in progress. This version has a new graphics interface to produce publication quality dendrogram.

The computing modules are limited to a maximum of 1400 populations, 150 groups, 1000 loci and 52 alleles per locus for allelic data, and limited by available Random-Access Memory (RAM) for quantitative data.