Automated alignment methods are clearly necessary and useful where large amounts of data are to be processed or in situations where no additional expert information is available. However, if a researcher is familiar with a specific sequence family under study, he or she may already know certain parts of the sequences that are functionally, structurally or phylogenetically related and should therefore be aligned to each other. In situations where automated programs fail to align these regions correctly, it is desirable to have an alignment method that would accept such user-defined homology information and would then align the remainder of the sequences automatically, respecting these user-specified constraints.