NMDS from SNP distance matrix

Question

[SushiRoll]

Hey all!

I'm trying to do an NMDS analysis of a group of samples, I have already computed a SNP distance matrix for every sample using a reference and would like to know if there is a way of inputting that for an NMDS analysis. I also have computed "ANI" pairwise distances between isolates using mash, I would be fine using that matrix as input distance. I have done NMDS in the past using MetaMDS from the Vegan package in R but my distance matrix was calculated using the presence/absence of certain phenotypes or genes.

Thanks!