A simulation module in the computer program COLONY for sibship and parentage analysis

A simulation module is built into the software package COLONY to simulate marker genotype data of individuals with a predefined parentage and sibship structure. The simulated data can then be used to compare the accuracy, robustness and computational efficiency of different methods for sibship and parentage reconstruction, to examine the impact of different parameter options in a software on its accuracy and computational efficiency and to assess the information sufficiency of a given set of markers for a sibship and parentage analysis. This computer note describes the method used for simulating genotype data with a pedigree and its possible applications. The method can quickly generate genotype data for a one- or two-generation pedigree of virtually any complexity with up to 30k offspring, at up to 30k codominant or dominant loci with an arbitrary degree of linkage and a user-defined mistyping rate. The data can be fed directly into the COLONY program for analysis by three sibship and parentage reconstruction methods and can also be imported into other programs such as Excel and R. With slight modification, the data can be analysed by other relationship analysis software.