3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
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15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
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20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>What's new ?</title>
27 <strong>What's new ?</strong>
30 Jalview 2.9 has been in development since December 2014. In addition
31 to a multitude of bug fixes and minor improvements (both small, and
32 rather big!), it also brings major new capabilities for codon-level
33 analysis of protein alignments and the retrieval and manipulation of
34 structural data.</p><p>For the full list of changes, see the
35 <a href="releases.html#Jalview.2.9">Jalview 2.9 Release Notes</a>.
38 <strong>Highlights in Jalview 2.9</strong>
40 <li><strong>Visualisation, editing and analysis of
41 cDNA and Protein alignments</strong><br />A new <a
42 href="features/splitView.html">Split View</a> window allows linked
43 protein and nucleotide sequence alignments to be viewed, edited,
44 and analysed as one. <br />cDNA alignments can also be
45 reconstructed from protein alignments calculated by Jalview's web
46 services, and update in response to edits in the amino acid view.<br />To
47 start experimenting with cDNA/Protein analysis, jut drop a file
48 containing cDNA sequences which code for proteins in an existing
49 alignment, and Jalview will do the rest.</li>
50 <li><strong>Enhanced Integration of UCSF Chimera</strong> <br>Jalview
51 2.9 provides full support for the use of Chimera to view 3D
52 structures linked to alignment views in the Jalview Desktop. We've
53 also included support for saving Chimera sessions in Jalview
54 project files.<br />Jalview and Chimera communicate using local
55 web server connections, which may cause firewall alerts on some
56 systems, but has the advantage of allowing bidirectional
57 communication. Communication between Jalview and Chimera is now
58 much more responsive, and selected regions in Chimera are now
59 shown as highlighted regions in the Jalview desktop.</li>
60 <li><strong>Interactive querying of the PDBe</strong><br />Jalview
61 users can now <a href="features/pdbsequencefetcher.html">browse</a> and <a href="features/viewingpdbs.html">retrieve 3D structure</a> data from the PDB
62 via the <a href="http://www.ebi.ac.uk/pdbe/api/doc/search.html">PDBe
63 Search API</a> (<a href="http://dx.doi.org/10.1093%2Fnar%2Fgkt1180">Gutmanas
64 et al 2014</a>). Developed in collaboration with the PDBe group at
65 EMBL-EBI, the interface allows both structured and free-text
66 queries to be performed, and allows automatic selection of the
67 most relevant structures for an alignment acording to a variety of
69 <li><strong>Improved support for RNA visualisation</strong><br />Jalview
70 2.9 integrates the latest version of the <a
71 href="features/varna.html">VARNA RNA Viewer</a>, and VARNA views
72 can also now be stored in Jalview projects. We've also dealt with
73 a number of lingering bugs in the VARNA/Jalview interface,
74 including the loss of pseudoknots when RNA secondary structure is
76 <li><strong>Protein Secondary Structure predictions
77 with JPred4</strong><br />Jalview includes a number of new features for
78 working with secondary structure predictions from the JPred4
79 server. These include new <a href="menus/popupMenu.html#hideinserts">popup menu actions</a> to automatically hide insertions and highlight
80 mutations in an alignment with respect to a <a href="calculations/referenceseq.html">Reference
81 Sequence</a>. Jalview 2.9's new <a href="io/export.html#htmlexport">scrollable
82 SVG HTML export</a> was also developed specifically for the JPred4