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 substitution matrices should, in theory, maximise alignment quality for an un-gapped alignment, and locally maximise quality for gapped alignments.