The main forces that affect the codon usage of EIAV. (A) The relationship between the effective number of codons (ENC) and the GC content of the third codon position (GC3). The continuous curve represents the expected curve between ENC value and GC3% in the absence of selection. All of spots lie below the expected curve. (ENC, GC3%) values of gag, pol and env were indicated by blue plot, green plot, and red plot respectively. (B) Correlation between G + C content at the first and second codon positions (GC12%) and that at synonymous third codon positions (GC3%). The line represents the correlation curve generated by the correlation analysis.