You may try with LDhat. I am not sure if there are newer software to estimate recombination, but LDhat should be fine if you only need an estimation.

For more information on how to run LDhat, check the manual on its webpage. In short, you need to run first the convert executable to generate a .locus and a .sites files. Then, use pairwise or one of the other models (see the manual) to estimate the recombination rates.