--- /dev/null
+<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
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+ * of the License, or (at your option) any later version.
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+<head>
+<title>Above PID Colours</title>
+<style type="text/css">
+<!--
+td {
+ text-align: center;
+}
+-->
+</style>
+</head>
+
+<body>
+ <p>
+ <strong>Colouring above a percentage identity threshold</strong>
+ </p>
+ <p>Selecting this option causes the colour scheme to be applied to
+ only those residues that occur in that column at least a certain
+ percentage of the time. For instance, selecting the threshold to be
+ 100 will only colour those columns with 100% identity, and selecting 50 will shade residues appearing in least 50% of the rows (or sequences) in each column.</p>
+ <p>The percentage calculation may include or exclude gaps in the column, depending on the option selected for the <a href="../calculations/consensus.html">consensus calculation</a>.</p>
+ <p>With a threshold of 0, colouring is unchanged.</p>
+</body>
+</html>
git://source.jalview.org / jalview.git / blobdiff