Hey there!
I was wondering if anybody knows any method that allows you to cluster sequences according to pairwise genetic distances. Ideally, I would be able to provide a genetic distance matrix and the method would group them, based on a cutoff also provided or optimised by the method according to the distribution of distances.
I'm interested on using my own genetic distances because I need to generate them with an alignment-free method so at the moment I'm using mash which uses k-mers (but of course I'd be open to suggestions). This is because many regions of my sequences don't share homology, and I'm interested on just clustering the most similar ones. I've tried creating trees but I don't want to rely on the topology to define a group (ie it doesn't have to be monophyletic).
Thanks a lot in advance for your hep!
Gon
