Alignment Quality Annotation
+Alignment Quality is one of the automatically calculated +quantitative alignment +annotations displayed below the columns of a multiple sequence +alignment (and can be used to shade the alignment). It is an ad-hoc +measure of the likelihood of observing the mutations (if any) in a +particular column of the alignment.
++More precisely, the quality score is inversely proportional to the +average cost of all pairs of mutations observed in a particular column +of the alignment - a high alignment quality score for a column would +suggest that there are no mutations, or most mutations observed are +favourable. +
+ +The Algorithm
+The quality score is calculated for each column in an alignment by
+summing, for all mutations, the ratio of the two BLOSUM 62 scores for
+a mutation pair and each residue's conserved BLOSUM62 score (which
+is higher). This value is normalised for each column, and then plotted
+on a scale from 0 to 1.
+
+Multiple alignment algorithms using the BLOSUM 62 substition matrices +should, in theory, maximise alignment quality for an un-gapped +alignment, and locally maximise quality for gapped alignments. +
+ +