Comparing 2 groups of bacterial genomes

Question

[Jonathon]

Hi there,

I have pacbio sequencing data for 4 bacterial genomes, these can be split into 2 groups of 2 based on their phenotype. I have annotated the genome and now have a list of genes present in each genome. I now want to compare these lists and identify genes that are present in one group of 2 but not in the other. I use R primarily along with some browser-based tools but I would greatly appreciate any suggestions.

Thank you