This archive contains initial output from analyses (including replicate runs). Folder 'BayEnv2_&_XtX' contains input files and files containing collected results for BayEnv2 analyses (five replicate runs) and XtX analyses (three replicate runs). Folder 'Bayescan' contains input file and output files from Bayescan analyses (four replicate runs). Folder 'HapFLK' contains output files from HapFLK analysis (29 separate chromosomes, 10 haplotype clusters defined). Folder 'LFMM' contains input files and output files from LFMM analyses (five replicate runs with three different variables: upstream catchment area, freshwater migration distance and run timing). Folder also contains results from PCA analysis to determined best K (in 'Tracey_Widom'). Folder 'XPEHH' contains raw and standard normalized XPEHH results for 29 chromsomes and 45 population comparisons.