Baculovirus: Molecular Insights on Their Diversity and Conservation

Figure 5

Baculovirus core gene variability. Histograms show the average PAM250 distances for each core gene with their corresponding standard deviations. These values were calculated using MEGA 4 program (UPGMA; bootstrap with 1000 replicates; gap/missing data = complete deletion; model = amino (dayhoff matrix); patterns among sites = same (homogeneous); rates among sites = different (gamma distributed; gamma parameter = 2.25)). PAM (point accepted mutation) matrices refers to the evolutionary distance between pairs of sequences. Given the weak similarity between several core proteins, PAM250 matrix was selected. The divergence considered in this matrix is 250 mutations per 100 amino acid sequence and was calculated to analyze more distantly related sequences. PAM250 is considered a good general matrix for protein similarity search.