The program ms_recomb, a modified version of Richard Hudson's ms, uses the coalescent to simulate genetic datasets with recombination rates that change through time. Richard Hudson kindly suggested changes to the code.
The program msstats_recomb, an extensively modified version of Kevin Thornton's msstats, implements n-tuple subsampling and calculates a suite of summary statistics with specific focus on recombination events. The code includes a new summary, min(dij), which shows some potential for detecting recombination rates through time. msstats_recomb requires a working installation of the libsequence library.
For details, see:
Cox, M.P., B.R. Holland, M.C. Wilkins and J. Schmid. 2013. Reconstructing Past Changes in Locus-Specific Recombination Rates. BMC Genetics 14:11. PDF, Supplemental Materials