I have whole bacterial genomes (very closely related) aligned and I would like to get the information of only the SNPs so that I can do some LD analysis. I would like to try to get them in the ped and map or plink formats preferably so that I can use them as imput for tassel. I haven't come across any tool that does this. The alignment is in nexus but I dont have a problem with any other msa format. Has any of you heard or had this issue?