I'm new to bioinformatics (i'm undergrad). I have 2 genomes, same species, probably different strains. I've used get_homologues to define the core genome, but i'm having trouble to find the singletons. I have already read several times both the manual and tutorial available and i've tried to used parse_pangenome_matrix to find which genes are present in A and absent in B, and it seems that there isn't any! (file with genes present in set A and absent in B (0) ).
How can it be possible, if the core genome is smaller than both genomes?
If they are the same species this is not so surprising.