In addition, our anchoring procedure can be used to obtain information for the further development of alignment algorithms. To improve the performance of automatic alignment methods, it is important to know what exactly goes wrong in those situations where these methods fail to produce biologically reasonable alignments. In principle, there are two possible reasons for failures of alignment programs. It is possible that the underlying objective function is 'wrong' by assigning high numerical scores to biologically meaningless alignments. But it is also possible that the objective function is 'correct' – i.e. biologically correct alignments have numerically optimal scores -and the employed heuristic optimisation algorithm fails to return mathematically optimal or near-optimal alignments. The anchoring approach that we implemented can help to find out which component of our alignment program is to blame if automatically produced alignments are biologically incorrect.