Robinson-Foulds metric implementation used for phylogenetic trees comparison (for homeodomain proteins, trees built with NJ and Muscle algorithms) for Computational Biology course at MIMUW.
On proteins from homeoDB (human, mouse, beetle and fruit fly), there is slight difference between trees built with Identitiy ClustalW and BLOSUM62 based Neighbour Joining alghortitm. Difference is about ~0.26