| Title || FREGENE |
| Short Description || FREGENE is a C++ program that simulates sequence-like data over large genomic regions in large diploid populations. |
| Long Description || 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.
The principle limitation of forward-in-time algorithms is computational, since the entire population must be tracked through time, not only the chromosomes that are ancestral to the observed sample. FREGENE implements many features to enhance computational efficiency, and includes a rescaling option that greatly reduces computation time at the cost of some approximation. |
| Project Started || 2007 |
| Last Release || 10 years, 6 months ago |
Chadeau-Hyam M, Hoggart CJ, O'Reilly PF, Whittaker JC, De Iorio M, Balding DJ, Fregene: simulation of realistic sequence-level data in populations and ascertained samples., BMC Bioinformatics, Sept. 8, 2008
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