Phylogeny-aware alignment with PRANK - Multiple Sequence Alignment Methods - page 153

Fig. 3 The phylogeny-aware algorithm distinguishes insertions from deletions and treats them differently. The
trees on the left represent the evolutionary histories of four short sequences undergoing two substitutions and
either an insertion (top) or a deletion (bottom). The trees on the right indicate how the alignment of sequences
is divided into three pairwise alignments, each creating an ancestral sequence (Z, Y, X) that is placed at the
corresponding internal node and then aligned pairwise with the next sequence. The classical alignment
algorithm penalizes the single insertion three times (indicated with filled triangle; open diamond and white
diamond with black dot denote match and mismatch, respectively); in contrast, the phylogeny-aware
algorithm implemented in PRANK flags the gapped site after the first alignment (indicated by filled diamond
above the sequence) and can then open a new gap at the flagged position without a further penalty (indicated
by curved right arrow). For a deletion, the gap needs to be created only once and the phylogeny-aware
algorithm removes the flag indicating the gap after the second alignment