I sequenced and assembled the genomes of two closely related species, and I would like to calculate the pairwise sequence divergence between the two whole genomes. I have done this for many orthologous genes extracted from the genome, but now I would like to align the whole genomes and calculate overall divergence. The genomes are in fasta format.
I know how to align the genomes and get a sam/bam file, and I know how to calculate sequence divergence between aligned fasta entries, but I am not sure how to link the steps. Is there a good way to get fasta-format alignments for whole genomes, or other ways to calculate their sequence divergence? (Bonus if there is a way to exclude coding regions stored in GFF files!)