RDP5 provides the option of generating random permutations of the user's input alignment to remove any signal of recombination. Applying recombination tests to the resulting permutations should approximate a null distribution of test statistics, which can be used to assess significance of tests on the original alignment. Note this will scale linearly with the number of permutations requested - on the other hand it should be trivial to parallelize.
RDP5 provides the option of generating random permutations of the user's input alignment to remove any signal of recombination. Applying recombination tests to the resulting permutations should approximate a null distribution of test statistics, which can be used to assess significance of tests on the original alignment. Note this will scale linearly with the number of permutations requested - on the other hand it should be trivial to parallelize.