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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
*
* This file is part of Jalview.
*
Jalview 2.9 has been in development since December 2014. In addition
to a multitude of bug fixes and minor improvements (both small, and
rather big!), it also brings major new capabilities for codon-level
- analysis of protein alignments and the manipulation of structural
- data.<br />For the full list of changes, see the <a
- href="releases.html#Jalview.2.9">Jalview 2.9 Release Notes</a>.
+ analysis of protein alignments and the retrieval and manipulation of
+ structural data.</p><p>For the full list of changes, see the
+ <a href="releases.html#Jalview.2.9">Jalview 2.9 Release Notes</a>.
</p>
<p>
<strong>Highlights in Jalview 2.9</strong>
-
<ul>
<li><strong>Visualisation, editing and analysis of
cDNA and Protein alignments</strong><br />A new <a
reconstructed from protein alignments calculated by Jalview's web
services, and update in response to edits in the amino acid view.<br />To
start experimenting with cDNA/Protein analysis, jut drop a file
- containing cDNA sequences which code for, and have IDs matching
- proteins in an existing alignment, and Jalview will do the rest.</li>
+ containing cDNA sequences which code for proteins in an existing
+ alignment, and Jalview will do the rest.</li>
<li><strong>Enhanced Integration of UCSF Chimera</strong> <br>Jalview
2.9 provides full support for the use of Chimera to view 3D
structures linked to alignment views in the Jalview Desktop. We've
much more responsive, and selected regions in Chimera are now
shown as highlighted regions in the Jalview desktop.</li>
<li><strong>Interactive querying of the PDBe</strong><br />Jalview
- users can now browse and retrieve 3D structure data from the PDB
+ users can now <a href="features/pdbsequencefetcher.html">browse</a> and <a href="features/viewingpdbs.html">retrieve 3D structure</a> data from the PDB
via the <a href="http://www.ebi.ac.uk/pdbe/api/doc/search.html">PDBe
Search API</a> (<a href="http://dx.doi.org/10.1093%2Fnar%2Fgkt1180">Gutmanas
et al 2014</a>). Developed in collaboration with the PDBe group at
criteria.</li>
<li><strong>Improved support for RNA visualisation</strong><br />Jalview
2.9 integrates the latest version of the <a
- href="http://varna.lri.fr">VARNA RNA Viewer</a>, and VARNA views
+ href="features/varna.html">VARNA RNA Viewer</a>, and VARNA views
can also now be stored in Jalview projects. We've also dealt with
a number of lingering bugs in the VARNA/Jalview interface,
including the loss of pseudoknots when RNA secondary structure is
shown VARNA.</li>
<li><strong>Protein Secondary Structure predictions
- with JPred4</strong>Jalview includes a number of new features for working
- with secondary structure predictions from the JPred4 server. These
- include the ability to automatically hide insertions and highlight
- mutations in an alignment with respect to a reference sequence.
- Jalview 2.9's new scrollable SVG HTML export mode was also
- developed specifically for the JPred4 server.</li>
+ with JPred4</strong><br />Jalview includes a number of new features for
+ working with secondary structure predictions from the JPred4
+ server. These include new <a href="menus/popupMenu.html#hideinserts">popup menu actions</a> to automatically hide insertions and highlight
+ mutations in an alignment with respect to a <a href="calculations/referenceseq.html">Reference
+ Sequence</a>. Jalview 2.9's new <a href="io/export.html#htmlexport">scrollable
+ SVG HTML export</a> was also developed specifically for the JPred4
+ server.</li>
</ul>
</body>
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