<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
- * 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.
*
Gruber, and Peter F. Stadler, <em>RNAalifold: Improved
consensus structure prediction for RNA alignments</em> (BMC
Bioinformatics, 9:474, 2008). Download the paper at <a
- href="http://www.biomedcentral.com/1471-2105/9/474"
- >http://www.biomedcentral.com/1471-2105/9/474</a>.
+ href="http://www.biomedcentral.com/1471-2105/9/474">http://www.biomedcentral.com/1471-2105/9/474</a>.
</p>
<p>
<strong>Running RNAalifold from Jalview</strong><br />
<Strong>RNAalifold prediction parameters</Strong> <br /> JABAWS and
Jalview only provide access to a selection of the RNAalifold
arguments. For a full description, see the documentation at <a
- href="http://www.tbi.univie.ac.at/RNA/RNAalifold.html"
- >http://www.tbi.univie.ac.at/RNA/RNAalifold.html</a>.
+ href="http://www.tbi.univie.ac.at/RNA/RNAalifold.html">http://www.tbi.univie.ac.at/RNA/RNAalifold.html</a>.
</p>
<p>
<strong>Supported Arguments which give alternate structures</strong>
Calculate an MEA structure where the expected Accuracy is computed
from the base pair probabilities. A more detailed description can be
found in the <strong>RNAfold</strong> program documentation at <a
- href="http://www.tbi.univie.ac.at/RNA/RNAfold.html"
- >http://www.tbi.univie.ac.at/RNA/RNAfold.html</a>.
+ href="http://www.tbi.univie.ac.at/RNA/RNAfold.html">http://www.tbi.univie.ac.at/RNA/RNAfold.html</a>.
</p>
<p>
<strong>Example RNAalifold Structure Annotation rows</strong>