HLA-HIV codon and HIV codon-HIV codon associations for the free plasma virus and PBMC proviral Pol sequences. Phylogenetic dependency network maps were generated with the PhyloDv software http://www.codeplex.com/MSCompBio. Each map shows HLA associations as tags pointing to their corresponding sites, and HIV codon-HIV codon associations as inner arcs connecting the associated sites. Plasma: all associations in free plasma virus from 250 patients that had a corresponding PBMC proviral sequence. Proviral: all associations for 250 PBMC proviral sequences. Conserved (shared): shared HLA-site or site-site associations between proviral and plasma sequences. If one amino acid at one site was associated with two different amino acids at another site (e.g. one for escape, one for reversion), only one association was counted. Unique plasma: associations only found to be significant in free plasma virus samples. Unique proviral: Associations only found to be significant in PBMC proviral samples. Significance was calculated with the binomial test; q-values are represented as a heat map shown in the lower inset. Associations with q < 0.2 are shown (all associations had p < 0.002). The upper inset table shows the number of significant associations in each map.