As described in our papers, DIALIGN constructs alignments from gapfree pairs of segments of the sequences. Such segment pairs are referred to as diagonals.

Every possible diagonal is given a so-called weight reflecting the degree of similarity among the two segments involved. The overall score of an alignment ist then defined as the sum of weights of the diagonals it consists of and the program tries to find an alignment with maximum score -- in other words: the program tries to find a consistent collection of diagonals with maximum sum of weights. This novel scoring scheme for alignments is the basic difference between DIALIGN and other global or local alignment methods. Note that DIALIGN does not employ any kind of gap penalty.

It is possible to use a threshold T for the quality of the diagonals. In this case, diagonals are considered only if their weights exceed this threshold, and regions of lower similarity are ignored.

In the first version of the program (DIALIGN 1), this threshold was in many situations absolutely necessary to obtain meaningful alignments. By contrast, DIALIGN 2 should produce reasonable alignments without a threshold, i.e. with T = 0. This is the most important difference between DIALIGN 2 and the first version of the program.

Nevertheless, it is still possible to use a threshold T, so it is up to the user to experience with this option.