In the multiple sequence alignment, what does the color of the amino acid letter mean?
The colors match the six amino acid types used in the CoC website. The amino acids are clustered into six physico-chemical groups: polar (N,Q,S,T), positive (K,R), negative (D,E), aliphatic (A,C,I,L,M,V), aromatic (F,H,W,Y), and special (G,P). These groups are not used in the calculations, but are shown to provide a guide to the properties of the amino acids in the alignment.
