Software to calculate expected sequence identity between two species, given speciation time

Question

[Biomonika (Noolean)]

I have two species, let's say one of them is human and second is one of the species of monkeys. If I align the homologous sequences between these two species, what's the expected sequence identity (given that I know speciation time as well as expected mutation rate)? Is there any software that would do this calculation for me?

I want to do this to verify that my alignments look reasonable.

[h.mon]

Do you want to perform this calculation genome-wide, or just for certain genes? Mutation rates vary widely throughout the genome.

Do you have reason to suspect your alignment is fishy? I would do a "poor's man" test, checking if annotated features (coding regions particularly) show good agreement.