scrm (sequential coalescent with recombination model ) is a coalescent simulator for biological sequences. Different to similar programs, it can approximate the Ancestral Recombination Graph as closely as needed, but still has only linear runtime cost for long sequences. It allows you to rapidly simulate chromosome scale sequences with essentially correct genetic linkage.
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scrm: efficiently simulating long sequences using the approximated coalescent with recombination.
Staab PR, Zhu S, Metzler D, Lunter G.
Bioinformatics. 2015 Jan 8. pii: btu861