inputBottleSiminputBottleSim creates automatically such input files. After BottleSim simulations are performed, a Genepop file containing genotypes of all replicates (each replicate is labelled as a different 'population') is produced, but alleles are coded in a different manner that makes comparison with the starting real data impossible (for instance, one may be interested in calculating Fst values between simulated populations and the real data). This function converts alleles back to their original sizes. It also allows the user to retain only a random subset of individuals for each replicate. Real and simulated data can subsequently be combined for analysis with the function combineBsim.outputBottleSim(datafile, subsample = 0)inputBottleSim. This will also create a file called 'alleles' in which all required information about allele numbers and sizes is stored. Once BottleSim simulations are done and a genotype file is obtained, it is necessary to put the 'alleles' file in the same directory as the BottleSim genotype output file before using this function.inputBottleSim, combineBsim