Figure 2. PCIs for each of four alignment types and two types of sequence distance.

The error bars indicate 95% confidence intervals, as calculated by the Wilson score interval [46]. The four alignment types used (indicated by different colors at the bottom) were multiple sequence alignment (which imposes an implicit pairwise global alignment on each pair of sequences), and global, semi-global, and local pairwise alignment. The two types of sequence distance used for each alignment method were alignment distance and evolutionary distance. (In fact, for a fixed alignment type and dataset, all evolutionary distances produced the same PCI as p-distance.) The green bars give the value of the barcode gap PCI.