![]() genodive is available for computers running Mac OS X 10. Genodive version 3.0 is a user-friendly program for the analysis of population genetic data. 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. ![]() Expected heterozygosity ( HS) was also calculated for each population using Genodive. The first line of the file is a comment line, which is written to the Description slot of the genambig object. that differ a lot of repeats in length (GenoDive manual). read.GenoDive imports data from text files formatted for this program. Table 1 Total alleles per primer, missing sample data, and number of triploids for Upper. This version presents a major update from the previous version and now offers a wide spectrum of different types of analyses. We used Genodive (Meirmans & Van Tienderen, 2004) to calculate the Weir and Cockerham unbiased weighted FST estimator (Weir & Cockerham, 1984) between all pairs of populations, with significance calculated using 10,000 permutations of the data. GenoDive is a Mac-only program for population genetic analysis that allows for polyploid data. Thus, the present data set includes two additional populations along with all populations studied by Rosenberg et al. 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. 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 (2 n = 8 x) for some analyses, but up to hexadecaploidy (2 n = 16 x) for other analyses. ![]() 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. 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. ![]()
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