Overview of SIA method. 1. Initial gappy alignment (The example shows an alignment of six sequences (A-F). "X" represents any amino acid; "-" represents a gap or missing data.); 2. The overlap-graph and two maximal cliques (green and purple); 3. Assignment of columns to cliques. The red column is placed in the smaller of the two cliques; 4. Two subalignments corresponding to the two cliques; 5. The resulting submatrices, and the combined matrix, of pairwise distances. Yellow cells are represented in both the green and purple submatrices. Orange cells must be imputed. ; 6. The phylogenetic tree estimated from the combined distance matrix. See text for details.