Introgression analyses

Question

[gubrins]

Heys, I'm working with whole-genome data of several non-model species and I'm studying the introgression patterns with Dsuite software (https://github.com/millanek/Dsuite). I have several samples per species from different localities and I was wondering if I should look for introgression patterns specifying each sample independently or clustering together the samples from the same species (it is allowed in the software). In my particular case, I am interested in a general pattern, so the second option would work, but I don't fully understand if it takes the common information of the several samples or what does it do.

Anybody worked with this software and can help me? Thanks in advance