Dear Renata. One of my friends talk to me about the Arlequin software in order to establish the identity cutoff (an analysis called Pairwise Sequence Comparison, or just PASC) but this software is very tricky (my personal opinion) for that reason I use the R package, through the use of the PEGAS module, specifically the MMD function (Mismatch distribution).
I'm using Geneious, but since it's a lot of sequences I would like a software to help me to do a graphic and visualize it better, to stablish a cutoof like it was made in the paper attached. I think that the R package should do that, I'm trying to figure it out how ;) thank you, guys (sorry for my English mistakes)
Christian, I don't think you can unless you buy it.. use the trial version for 14 days or keep the basic version ;) I'm considering to buy it, it's expensive but I think it's worth it