Reconciling recombination events

[ArtPoon]

From Darren:

OpenRDP does not seem to make an attempt to reconcile recombination
events that yielded the detected recombinant sequences with the recombinant
signals it detects. From what I understand, with OpenRDP if two sequences
in a datasets are both descended from an ancestral recombinant they will
not be identified as sharing evidence of the same ancestral
recombination event. Is that right? I couldn't see any code in openRDP for
reconciling/mapping the multitudes of detectable recombination signals
to individual actual recombination events.

First step is to locate this functionality in the RDP code that was provided