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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
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