CodonRecSim is an old program of mine for simulating samples in a codon based models under the coalescent with recombination. This program was used in Anisimova, M., R. Nielsen and Z. Yang. 2003 Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites. Genetics 164: 1229-1236. It is not very well-supported - but if you are used to simulating samples using Evolver distributed in the PAML package by Ziheng Yang - you may be able to figure out how this program works. Most of the interface is modelled based on evolver - and in many analyses it should be able to work just as evolver but with an extra parameter: R - the population scaled recombination rate. However, there are a number of evolver options that are not implemented in the program. Notice that some code in this program is copyrighted to Ziheng Yang.