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Frequent Toggling between Alternative Amino Acids Is Driven by Selection in HIV-1

Figure 2

Simulation along HIV-1 nef phylogeny.

Data was simulated under purifying selection, neutrality, diversifying selection, or toggling to evaluate power and false positives rates. (A) Amino acid sequence logos [73] of ten randomly drawn codon sites for each category of simulated site. (B) Simulated toggling site mapped to HIV-1 phylogeny showing the occurrence of escape (red arrows) and reversion (green arrows) mutations. (C) Simulated diversifying selection site mapped to HIV-1 phylogeny.

Figure 2