Fast development of new heuristic methods solving a multiple sequence alignment~(MSA) problem enforces a
development of benchmarks for evaluation of the quality of these methods. One of the most reliable benchmarks relies on
a comparison of an alignment created by a tested method and the reference alignment (which is usually created on the
basis of some additional knowledge like its tertiary structure) stored in the database. This paper surveys methods for the
quality evaluation of multiple sequence alignment based on databases of reference alignments. Several classes of
reference alignments have been defined. Then, applicable quality measures for these classes have been described. We
have also presented applications which can be used to perform the evaluation of the quality of a tested alignment. Among
others, this survey contains our remarks and observations concerning reference alignments, the quality measures and the
applications for the quality evaluation. Based on our experience, we have proposed a new nomenclature for quality
measures. To clarify described problems, two example calculations of various measures for several classes of the
reference alignments are presented in the Appendix.
Keywords: Databases of reference alignments, evaluation of MSA, multiple sequence alignment.
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