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<head><title>Alignment Quality Annotation</title></head>
<body>
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
+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><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
+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>
git://source.jalview.org / jalview.git / blobdiff