Figure 3

Use case 2. Identify synonymous and nonsynonymous variations. Integrated visualization of codon (top panel) and amino-acid (bottom panel, colored by chemical groups) alignments, with individual sequences arranged according to the genome phylogeny, allows identification of synonymous and nonsynonymous variations. This view also facilitates exploration of selective mechanisms underlining sequence variations. Here, three notable patterns of sequence variability are highlighted for the first 44 codons of ospC. Some sites vary synonymously within and between species (high-lighted in blue), indicating strong purifying selection. Two sites vary non-synonymously within a single species (in orange), suggesting balancing selection. The first 21 sites (in red) are nearly constant not only in amino acids but also in codons, hinting strong selection for codon usage in this gene region.