Comparative genomics between model organism and non-model organism

Question

[Ric]

Hello,

I have two genomes in fasta format. One is for a model organism and the other one is for non-model organism. Furthermore, I have transcriptome data.

What is the best way to compare two genomes to each other and also to take advantage of Busco http://busco.ezlab.org?

Thank you in advance.

Mic

[Mehmet]

Can you make your questions more specific? What do you want to compare in two genomes?

[Prakki Rama]

Hi could you find a way? Could you please share if yes.