Figure 3. Two alignments (left and right) which make the same homology statements and therefore are both represented by the same POSET (center).

“The mathematics of distance-based alignment” in Text S1 discusses this view of alignments as POSETs. The alignment on the right minimizes the number of gap-open events and as such is appropriate for analyses such as inferring parsimonious indel frequencies across a clade. Alignments are displayed with TeXshade [63].