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GenoDive v. 3.0: Easy-to-use software for the analysis of genetic data of diploids and polyploids.

GenoDive v. 3.0, is a user-friendly program for the analysis of population genetic data. This version presents a major update from the previous version and now offers a wide spectrum of different types of analyses. GenoDive has an intuitive Graphical User Interface that allows direct manipulation of the data though transformation, imputation of missing data, and excluding and including individuals, population and/or loci. Furthermore, GenoDive seamlessly supports 15 different file formats for importing or exporting data from or to other programs. One major feature of GenoDive is that it supports both diploid and polyploid data, up to octaploidy (2n=8x) for some analyses, but up to hexadecaploidy (2n=16x) for other analyses. The different types of analyses offered by GenoDive include multiple statistics for estimating population differentiation (φ , F , F' , G , G' , G'' , D , R , ρ), AMOVA-based K-means clustering, Hardy-Weinberg equilibrium, hybrid index, population assignment, clone assignment, Mantel test, Spatial Autocorrelation, 23 ways of calculating genetic distances, and both PCA and PCoA. A unique feature of GenoDive is that it can also open datasets with non-genetic variables, for example environmental data or geographical coordinates that can be included in the analysis. In addition, GenoDive makes it possible to run several external programs (LFMM, Structure, Instruct, and vegan) directly from its own user interface, avoiding the need for data reformatting and use of the command line. GenoDive is available for computers running Mac OS X 10.7 or higher and can be downloaded freely from: http://www.patrickmeirmans.com/software.

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