Software to calculate expected sequence identity between two species, given speciation time
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.
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Biomonika (Noolean)
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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.