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1. Admixture_scripts Admixture_scripts Public

   Scripts used to plot results from Admixture, as well as a README with directions for how to generate said results.

   Python 1

2. filter_SNPs_maxMAF filter_SNPs_maxMAF Public

   Small pipeline to calculate minor allele frequency (MAF) by SNP, used here to filter to 1 SNP per locus based on max MAF

   Python 1

3. plot_fineRADstructure plot_fineRADstructure Public

   R markdown designed to build a fineRADstructure plot that includes, coancestry heatmap, dendrogram, and colorbar 'labels' for individuals (this is done manually by means of whitelist, according to …

   R 1

4. Isolation_by_distance_scripts Isolation_by_distance_scripts Public

   R Markdown script to produce an isolation by distance figure. Requires a genepop file of SNPs and a list of coordinates for each population. The coordinate list should have the same order as the ge…

5. Pairwise_FST_figure_scripts Pairwise_FST_figure_scripts Public

   R Markdown document with code to produce a pairwise FST heatmap. This will a data frame of pairwise FST values, which I chose to produce in Arlequin. See Arlequin documentation README for mor infor…

6. Phylogenetic_tree_scripts Phylogenetic_tree_scripts Public

   R Markdown document with code to produce phylogenetic trees from a genepop file.