-<html>\r
-<head><title>Alignment Quality Annotation</title></head>\r
-<body>\r
-<p><strong>Alignment Quality Annotation</strong></p>\r
-<p>Alignment Quality is one of the automatically calculated\r
-quantitative alignment\r
-annotations displayed below the columns of a multiple sequence\r
-alignment (and can be used to shade the alignment). It is an ad-hoc\r
-measure of the likelihood of observing the mutations (if any) in a\r
-particular column of the alignment.</p>\r
-<p>\r
-More precisely, the quality score is inversely proportional to the\r
-average cost of all pairs of mutations oberved in a particular column\r
-of the alignment - a high alignment quality score for a column would\r
-suggest that there are no mutations, or most mutations observed are\r
-favourable.\r
-</p>\r
-\r
-<p><em>The Algorithm</em><br>\r
-The quality score is calculated for each column in an alignment by\r
-summing, for all mutations, the ratio of the two BLOSUM 62 scores for\r
-a mutation pair and each residue's conservered BLOSUM62 score (which\r
-is higher). This valueis normalised for each column, and then plotted\r
-on a scale from 0 to 1.\r
-</p>\r
-<p>\r
-Multiple alignment algorithms using the BLOSUM 62 substition matrices\r
-should, in theory, maximise alignment quality for an un-gapped\r
-alignment, and locally maximise quality for gapped alignments.\r
-</p>\r
-</body>\r
-</html>\r
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * 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
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * 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>
git://source.jalview.org / jalview.git / blobdiff