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- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
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* This file is part of Jalview.
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-<head><title>Alignment Quality Annotation</title></head>
+<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>
+ <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 substition matrices
-should, in theory, maximise alignment quality for an un-gapped
-alignment, and locally maximise quality for gapped alignments.
-</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 substition
+ matrices should, in theory, maximise alignment quality for an
+ un-gapped alignment, and locally maximise quality for gapped
+ alignments.</p>
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git://source.jalview.org / jalview.git / blobdiff