I'm very new to this subject, but my current task is to try to detect any level of recombination in a supposedly asexual haploid species (as a proxy for cryptic sex, maybe). I have information for a number of loci (5-7) for some populations. There seem to be a great variety of methods out there, but could you talk about your favorites? Also, how do you normally deal with indels for this? Do you discard them, or code them in some way?

Thanks in advance!