I am trying to build some phylogenetic trees based on core genome SNPs in bacteria using parsnp. However, I have a doubt. If I include only my strains in the alignment then my tree will be unrooted. If I want a rooted tree then I will have to include an out-group. However, if I include the out-group then my core genome is not accurate anymore, as I will be cutting it down considerably. Any thoughts about this matter? I am really confused!