Haplotype coloring. The default haplotype block mosaic, which minimizes total color transitions across the entire genome, is shown above. Below is the selected subset of strains recolored according to their displayed order. The topmost strain is assigned a single color and subsequent strains are assigned the same color where their haplotypes match the first strain. A strain is assigned a second color where it does not match the first strain and subsequent strains are assigned the color where they match the new strain but not the first. This process is repeated for all remaining strains in displayed order. This recoloring highlights the haplotype similarities over extended genomic regions (60 Mbases as shown) between the selected strains.