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-<head><title>Alignment Quality Annotation</title></head>
-<body>
-<p><strong>Alignment Quality Annotation</strong></p>
-<p>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.</p>
-<p>
-More precisely, the quality score is inversely proportional to the
-average cost of all pairs of mutations oberved 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.
-</p>
-
-<p><em>The Algorithm</em><br>
-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 conservered BLOSUM62 score (which
-is higher). This valueis normalised for each column, and then plotted
-on a scale from 0 to 1.
-</p>
-<p>
-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.
-</p>
-</body>
-</html>
+-->
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