Figure 5
From: Grammar-based distance in progressive multiple sequence alignment
Adjust gaps. Gaps in the complete MSA ensemble A are grouped together via a sliding window. After the histogram H of gaps-per-column is generated, an equidistant column-window is shifted across the alignment, moving one column per interval. If the center column contains more gaps than some parameter threshold, the columns within the window are scanned for possible gaps that may be shifted into the center column. The resulting adjusted ensemble A Adj is presented as the final alignment.