forqs is a forward-in-time population genetics simulation that tracks individual haplotype chunks as they recombine each generation. forqs also also models quantitative traits and selection on those traits.
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Bioinformatics. 2014 Feb 15;30(4):576-7. doi: 10.1093/bioinformatics/btt712. Epub 2013 Dec 10.
forqs: forward-in-time simulation of recombination, quantitative traits and selection.
Kessner D1, Novembre J.