![]() genodive is fully multithreaded, which means that all calculations are performed in the background, keeping the user interface responsive and available for other tasks. Although genodive does not show any graphical output, great care has been taken to ensure that all output is tab‐delimited so that the results can be easily plotted using spreadsheet software such as excel or using r.īehind the user‐friendly GUI of genodive is a computational core that makes full use of the power of both laptop and desktop computers. Besides subsetting, genodive provides other ways of data manipulation: transformation, recoding of alleles, subsampling to a single ploidy level, and smart imputation of missing data. Furthermore, subsetting the data makes it possible to easily assess the influence of possible erratic individuals or loci on the outcome of the analysis. This in‐ and excluding allows for testing hypotheses that pertain to only a subset of the data, for example only populations from a certain region or only individuals with a certain ploidy level. Furthermore, there is a “Special Include” dialogue that allows the user to include or exclude observations based on a specific set of criteria, such as including loci or individuals based on the percentage of missing data, including populations based on the number of samples, or including only a single individual per clone (one ramet per genet). The GUI has checkboxes for every individual, population and locus that can be clicked to include or exclude them from the analysis. 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 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 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. 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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