Figure 6. 9-codon Sliding Window Analysis of Passage 5 Viral Genes.

π_N (black) and π_S (red) of the passage 5 mice were calculated for each gene using a 9-codon sliding window analysis by SNPgenie. Multiple π_S peaks were identified in each gene, with relatively low respective π_N values, which indicate regions that may be crucial to the fitness of SIVsm. Alternatively, in other locations across multiple genes, particularly vif and nef, there are regions with markedly higher π_N values relative to π_S, which is indicative of diversifying selection.