One result of our study is that anchor points can not only improve the biological quality of the output alignments but can in certain situations lead to alignments with significantly higher numerical scores. This demonstrates that the heuristic optimisation procedure used in DIALIGN may produce output alignments with scores far below the optimum for the respective data set. The latter result has important consequences for the further development of our alignment approach: it seems worthwile to develop more efficient algorithms for the optimisation problem that arises in the context of the DIALIGN algorithm. In other situations, the numerical scores of biologically correct alignments turned out to be below the scores of biololgically wrong alignments returned by the non-anchored version of our program. Here, improved optimisation functions will not lead to biologically more meaningful alignments. It is therefore also promising to develop improved objective function for our alignment approach.