bacterium Gene Ontology From whole genome sequencing

Question

[cabraham03]

Hi, I have 21 genomes (whole genome sequencing Of Vibrio vulnificus) and I will like to determinate the differences in GO terms Among 2 groups (12 genomes for group 1, and 9 genomes for group 2) so I will like to know how can I do it, it’s any pipeline than you can send or recommend me !!!?? Or any command line software that can I use, with the genomes in fastq/fasta format (I have each genome in contigs, assembled with spades, and the proteins obtained from prodigal for each genome).

Thanks so much !!