+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
+<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 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.</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
+ conserved BLOSUM62 score (which is higher). This value is normalised
+ for each column, and then plotted on a scale from 0 to 1.
+ </p>
+ <p>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.</p>
+</body>
+</html>