Screenshot of local nef alignment. Jalview screenshot of positions 402 to 510 of the alignment of 66 nef sequences. Identical letters (A, C, G or T) that are of the same color and on the same column, come from the same MS4 class. (It can happen that two neighboring colors are hard to distinguish). In the left column, the sequences are identified by their accession number, the type of virus (HIV1 or 2, SIV-CPZ or SMM) the group -for example HIV-1 M, N, O or HIV-2-A, the subtype, and the subtype in the case of HIV-1-M/C, for example. The sites that are not colored belong to classes with only one element.