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22 <head><title>Alignment Quality Annotation</title></head>
24 <p><strong>Alignment Quality Annotation</strong></p>
25 <p>Alignment Quality is one of the automatically calculated
26 quantitative alignment
27 annotations displayed below the columns of a multiple sequence
28 alignment (and can be used to shade the alignment). It is an ad-hoc
29 measure of the likelihood of observing the mutations (if any) in a
30 particular column of the alignment.</p>
32 More precisely, the quality score is inversely proportional to the
33 average cost of all pairs of mutations observed in a particular column
34 of the alignment - a high alignment quality score for a column would
35 suggest that there are no mutations, or most mutations observed are
39 <p><em>The Algorithm</em><br>
40 The quality score is calculated for each column in an alignment by
41 summing, for all mutations, the ratio of the two BLOSUM 62 scores for
42 a mutation pair and each residue's conserved BLOSUM62 score (which
43 is higher). This value is normalised for each column, and then plotted
44 on a scale from 0 to 1.
47 Multiple alignment algorithms using the BLOSUM 62 substition matrices
48 should, in theory, maximise alignment quality for an un-gapped
49 alignment, and locally maximise quality for gapped alignments.