Visualization of reference (a) and reconstructed (bcd) alignments for test case BB40037 . In all alignments sequences are ordered accordingly. Each sequence is colored based on the evolutionary distance to its neighbors in a phylogenetic tree, such that families of related sequences have similar colors. Trees for (a) and (b) are computed with the PhyML 3.0 program , using the maximum parsimony method. Trees for (c) and (d) are the guide-trees used by those aligners.