Phylogenetic analysis and splits tree of the HIV GAG-POL for different brain regions of patient A. (a). Phylogenetic analysis based on the nucleotide sequence of the 325 bp region of HIV-1 GAG-POL from patient A. HIV-1 JRCSF was used as an outlier. (b). Splits tree phylogenetic reconstruction based on the protein sequence of the pol region. As the 325 bp nucleotide sequence contained 2 separate overlapping coding regions of the Gag and Pol genes, we excised the first 45 nucleotide bases from the alignment for translating the Pol section of the gene to amino acids for phylogenetic reconstructions. The tree shows inter-phylogenetic relationships based on single amino acid changes (shown for each region and between regions at appropriate branches along with positions). F: frontal, H: hippocampus, B: basal ganglia.