I am using Reciprocal Best Hits (RBH) method to group orthologous proteins from diverse species. I have 50 eukaryotic species at hand, so should do 49x50 BLASTs. I found it needs much time, even setting evalue = 1e-5 and getting top hit.
Is there any way to improve my work? I learned some parallel technology is powerful, but don't know how to start. Any of your suggestions will be appreciated. THANK YOU very much!