I have aligned genes in one species to genes in another and would like to find out how many genes of the query are presents in the target.
To do this, I have used Exonerate. I am able to output the percentage identity using Exonerate. However, to have a more robust measure of whether genes correspond to one another in each species, I would like to E-values. Is there a way to output these in Exonerate?
I am also unsure of where to set my threshold for percentage identity. I know both of these species had a common ancestor if that is any help?