Figure 1. Schematic representation of the MDS analysis.

The analysis of N active and N _sup supplementary sequences are represented in blue and orange, respectively. D and D_sup represent distance matrices, S and S_sup cross-product matrices and F and F_sup factor score matrices. The coordinate of the i ^th active sequence on the k ^th principal component is directly obtained from the i ^th element of the k ^th column of F. The coordinate of the j ^th supplementary sequence on the k ^th principal component of the active space is directly obtained from the j ^th element of the k ^th column of F_sup. The numbers above the arrows refer to the equations given in the Methods section.