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FREGENE is a C++ program that simulates sequence-like data over large genomic regions in large diploid populations. Unlike coalescent-based simulation tools, such as MS (Hudson, 2002), FREGENE works forwards-in-time which allows a wide range of demographic and selection scenarios to be implemented. Many such models are already incorporated into FREGENE, and since it is open source users can modify or extend these. Coalescent methods have difficulty incorporating large amounts of gene conversion or crossover (Hoggart et al. 2007), whereas these pose no particular problem for FREGENE. FREGENE offers a flexible model for recombination hotspots, and can readily simulate regions up to tens of Mb on a standard desktop computer.

Project website:

The following Modules files should be loaded for this package:

module load fregene/fregene-2008