rdp4.txt

The “require topological evidence” setting allows you to specify
whether or not you want the program to discard recombination signals
that have no phylogenetic support. While this might seem an obvious
thing to do, you should realise that many of the recombination
detection methods implemented in RDP4 are fully capable of detecting
real recombination events that do not result in any detectable change
in phylogenetic tree topologies along an alignment. The default setting
is that topological evidence is required but this is simply because most
users (for good or bad reasons) would find this setting most desirable.