Search for: [Abstract = "We do not claim that one of these measures is better than the other, but they are definitely different. Such a situation can be the source of confusion when alignments obtained using various methods are compared. Therefore, we propose a new nomenclature for the measures of the quality of multiple sequence alignments to distinguish which one was actually calculated. Moreover, we have found that the occurrence of a gap in some column in the first sequence of the reference alignment causes column discarding."]

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