The method used to present the results of the calculation of an optimal pairwise alignment score. The matrix field (i,j) is the score assigned to the optimal alignment between two residues (up to a total of i by j residues) from the input sequences. Each entry is calculated from the top-left neighboring entries by way of a recursive equation.
In mathematics, a distance matrix is a matrix (two-dimensional array) containing the distances, taken pairwise, of a set of points. It is therefore a symmetric N×N matrix containing non-negative reals as elements, given N points in Euclidean space. The number of pairs of points N×(N-1)/2 is the number of independent elements in the distance matrix.