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Table 2 a Consensus V3 amino acid sequences of subtypes A1 and D from Uganda with pairwise entropy comparison at each site, and b V3 sequences of outgroup sequences to subtype D in Uganda

From: A large population sample of African HIV genomes from the 1980s reveals a reduction in subtype D over time associated with propensity for CXCR4 tropism

  1. The Entropy-Two tool from the Los Alamos National Laboratory database was used to compare Shannon’s Entropy at each codon position (indicating variability at each position). Sites with significantly different (p < 0.01) entropy between the subtype A1 consensus and the subtype D consensus are highlighted in bold. Positively charged amino acids (K, Lys) and (R, Arg) are shown in blue, while negatively charged amino acids (D, Asp) and (E, Glu) are shown in red, geno2pheno predictions are shown to the right