Additional file 5 of Analysis of lineage-specific protein family variability in prokaryotes combined with evolutionary reconstructions

Additional file 5: Fig. S4. Amino acid frequency PCA for conserved and variable positions for families from Table 2. High- (V > 2) and low-variable (V < 0.5) sites were extracted from the alignments of 34 csCOGs (Additional file 4: Fig. S3); relative frequencies of amino acids were computed for all 68 (34 × 2) subsets. Principal Component Analysis of amino acid frequencies was performed using the prcomp function of R package. The plot shows the location of the high- (red circles) and low-variable (cyan triangles) and the contributions of individual amino acids (blue arrows) in the plane of the first two principal components