<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
<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 more than a certain
- percentage of the time. For instance selecting the threshold to be
- 100 will only colour those columns with 100 % identity. This
- threshold option can be applied to the Zappo, Taylor, Hydrophobicity
- and User colour schemes.</p>
+ 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