I am comparing whole genomes of a closely related species using Nucmer. I want to calculate the %of similarity based on the bases aligned from each genome using Bray-Curtis dissimilarity (I had also tried Sorensen coefficient). The problem is that some genomes have very different genome sizes (let's say ranging from 40 Mb to 170 Mb). In those cases, I get similarity values above 1 (or 100%) which is impossible. I have tried some normalizations as those recommended by Somerfield 2008, and Yoshioka (2008) but nothing worked.
Some suggestions? alternatives?