I don't know an answer, but you might find it useful to ask the question on the Quora.com website. If you have any difficulty I could ask it for you there. I see the other answer here is a bit old, though not necessarily too old.
By the way, most people only have one genome. Claiming to have two appears to be arrogant!
It would truly be of so kind of you on the off chance that you share this to Quora!
Well, I have those two genomes not inside my nucleus, but stored in my PC! Additionally, if you are unsure about the existence of any organisms, you know, most the higher living beings are now referred as metaorganism! In a sense, all of these organisms are bearing multiple nested genomes within their own large genome!
Indeed but my humor effort wouldn't work if I took account of mitochondria and chimera, not to mention I didn't want to brag that I have trillions of genomes in my own brain alone.
I guess the question can be "What's [the] best software to find genes shared between genomes?".
Some questions get no answers but usually ones about software do.