Our software provides two slightly different options for using anchor points. There is a strong anchoring option, where the specified anchor positions are necessarily aligned to each other, consistency provided. The remainder of the sequences is then aligned based on the consistency constraints given by these pre-aligned positions. This option can be used to enforce correct alignment of those parts of the sequences for which additional expert information is available. For example, we are planning to align RNA sequences by using both primary and secondary structure information. Here, locally conserved secondary structures could be used as 'strong' anchor points to make sure that these structures are properly aligned, even if they share no similarity at the primary-structure level.