Most importantly, genodive makes it very easy to create a subset of the data. When data have been loaded successfully, the GUI of genodive provides extensive tools for manipulating the data (see Figure 1 for some examples).
GENODIVE FST SERIES
genodive also has its own file format that allows for some features that are unique to genodive, such as support for mixed ploidy data, clone assignments and multiple series of population groups. File formats recognized by genodive are bayesass (Wilson & Rannala, 2003), convert (Glaubitz, 2004), fstat (Goudet, 1995), genalex (Peakall & Smouse, 2006), genepop (Raymond & Rousset, 1995), genetix (Belkhir, Borsa, Chikhi, Raufaste, & Bonhomme, 2004), migrate (Beerli & Felsenstein, 1999), spagedi (Hardy & Vekemans, 2002) and structure (Pritchard, Stephens, & Donnelly, 2000) in addition, files can be exported in the formats of aflp‐surv (Vekemans, 2002), arlequin (Excoffier & Lischer, 2010), bayescan (Foll & Gaggiotti, 2008), lfmm (Frichot, Schoville, Bouchard, & Francois, 2013) and tess3 (Caye, Deist, Martins, Michel, & Francois, 2015). genodive automatically recognizes which format a text file is in and reads the data, without any need for dialogues.
This circumvents tedious recoding of text files from one format to the other, or the use of third‐party tools to do such reformatting. Genodive can seamlessly import and export data in a wide variety of formats. The genodive user interface, with its most important features explained
GENODIVE FST MAC OS X
genodive is available for computers running Mac OS X 10.7 or higher and can be downloaded freely from. 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. A unique feature of genodive is that it can also open data sets with nongenetic variables, for example environmental data or geographical coordinates that can be included in the analysis. The different types of analyses offered by genodive include multiple statistics for estimating population differentiation ( φ ST, F ST, Fʹ ST, G ST, Gʹ ST, Gʹʹ ST, D est, R ST, ρ), analysis of molecular variance‐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 principal components and principal coordinates analyses. One major feature of genodive is that it supports both diploid and polyploid data, up to octaploidy (2 n = 8 x) for some analyses, but up to hexadecaploidy (2 n = 16 x) for other analyses. Furthermore, genodive seamlessly supports 15 different file formats for importing or exporting data from or to other programs. genodive has an intuitive graphical user interface that allows direct manipulation of the data through transformation, imputation of missing data, and exclusion and inclusion of individuals, population and/or loci.
GENODIVE FST UPDATE
This version presents a major update from the previous version and now offers a wide spectrum of different types of analyses. Genodive version 3.0 is a user‐friendly program for the analysis of population genetic data.
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