Thus, alignment programs can be evaluated by their ability to correctly align these core blocks. BAliBASE covers various alignment situations, e.g. protein families with global similarity or protein families with large internal or terminal insertions or deletions. However, it is important to mention that most sequences in the standard version of BAliBASE are not real-world sequences, but have been artificially truncated by the database authors who simply removed non-homologous C-terminal or N-terminal parts of the sequences. Only the most recent version of BAliBASE provides the original full-length sequence sets together with the previous truncated data. Therefore, most studies based on BAliBASE have a strong bias in favour of global alignment programs such as CLUSTAL W [1]; these programs perform much better on the BAliBASE data than they would perform on on realistic full-length protein sequences. The performance of programs that are based on local sequence similarities, on the other hand, is systematically underestimated by BAliBASE. Despite this systematic error, test runs on BAliBASE can give a rough impression about the performance of multiple-alignment programs in different situations.