I have been using MEGA to calculate the Ka/Ks for genes between 5 species. Is there a statistical test I should be using to determine if the ratio is significantly different from neutral evolution (Ka/Ks = 1)? I've seen mention of using a Fisher's Exact Test, but I'm not understanding how to go about this.
If you want to compare uniqueness or overlaps between genes of different species, you could try bedtools fisher for the combinations between 5 species. Bedtools fisher works between two samples, so, if you want to find pairs of two (in which order does not matter) should be 10 combinations. Bedtools fisher could be run 10 times, and the ratios could be compared.