Protease and RT phylogenetic dependency network for the Mexican cohort. A phylogenetic dependency network map was generated with the PhyloDv software http://www.codeplex.com/MSCompBio. Pol positions are drawn counter clockwise, with the N-terminus of the protease at the 3 o'clock position, and the first RT codon corresponding to position 100. Lines indicate associations between codons (inside the circle) or between HLA alleles and codons (outside the circle). Colors indicate q-values of the most significant associations between two attributes. Associations with q < 0.2 for 280 individuals from Central/Southern Mexico were included.