Plots of amino acid and nucleotide diversity in the HIV full-length genome. (A) Amino acid diversity along the HIV full-length genome using the sliding windows (window size: 100AA; also see the plots of exact diversity values in Additional file 1: Figure S5). Each colored plot shows the density of amino acid diversity for one HIV group, subtype or CRF genome, indicated by the figure legend. Six layers are shown beneath the plots: (1) HIV-1 protein regions (HXB2 reference) are concatenated and shown with abbreviated names (e.g. MA: matrix); (2) peptide-inhibitor-derived region; (3) CD8+ T cell epitope position; (4) CD4+ T cell epitope position; (5) antibody epitope position; (6) HIV-2 protein region (BEN reference). (B) Nucleotide diversity along the full-length HIV genome using sliding windows (window size: 300 nucleotides; also see the plots of exact diversity values in Additional file 1: Figure S6). Each colored plot shows the density of nucleotide diversity for one HIV group, subtype or CRF genome, indicated by the figure legend. Annotated HIV-1 and HIV-2 reference genomes are shown beneath; each track contains one open reading frame (ORF). Long terminal regions in the HIV genome are not shown. (C) Contour map of inter-clade amino acid diversity between HIV-1 subtype B and the other HIV genomes. Inter-clade amino acid diversity was calculated by a sliding window of 30 amino acids over the HIV genome (low: ≤1 AA difference, high: ≥25 AA differences). Five colored layers beneath the contour map are annotated similarly in (A).