</head>
<body>
<p>
- <strong>Jalview 2.11.1.0</strong>
+ <strong>Welcome to Jalview Version $$Version-Rel$$ !!</strong> <br />Please
+ take a look at the <a href="releases.html#Jalview.$$Version-Rel$$">release
+ notes</a> for this build. Read on for the highlights.
</p>
<p>
- Jalview 2.11.1.0 is the first minor release for the 2.11 series.
- Along with a number of critical bug fixes and improvements it brings
- new functionality for mapping sequence features between CDS and
- Protein alignments. It is also the first release made under a new <em>four</em>
- number versioning scheme, which will allow us to keep track of
- patches and bug fixes.
+ <strong>Highlights in 2.11.2</strong>
</p>
- <ul>
- <li><strong>Virtual Features</strong><br />In previous
- versions of Jalview, specific nucleotide sequence features such as
- genomic variants and exons were transferred to protein products on
- import. Jalview 2.11.1 instead provides 'virtual features' that
- can be enabled and overlaid on linked CDS/Protein views via their
- <a href="features/splitView.html#virtualfeats">Sequence
- Features dialog</a>. This allows more analyses of nucleotide and
- peptide sequence features on alignments in a more flexible and
- memory efficient way than in earlier versions.</li>
- <li><strong>Improved VCF data import</strong><br /> <a
- href="features/importvcf.html#attribs">Standard attributes for
- filtering variants</a> (e.g. position, QUAL field etc) are now
- extracted from VCF files. This new feature was suggested by a user
- at the Jalview booth during ISMB 2019.</li>
- <li><strong>Extended feature attributes are exported
- in GFF3</strong><br />Complex attributes from VCF files can be exported
- and imported via GFF3</li>
- <li><strong>Updated Jalview Installer and Launcher</strong><br />Jalview's
- installation packages are now built with Install4j 8, which brings
- better support for Linux and improved control of file
- associations. New <a href="memory.html#jvm">parameters on the
- Jalview launcher</a> allow an upper memory limit to be specified <em>via</em>
- a Jalview launch file, to prevent it from hogging your system.</li>
- </ul>
<p>
- See the <a href="releases.html#Jalview.2.11.1.0">2.11.1.0
- release notes</a> for full details of bugs fixed and new known issues.
+ <strong>New features for working with 3D Structure</strong><br />
+ Jalview 2.11.2 features a number of new capabilities described
+ below.
+ </p>
+
+ <p>
+ <strong>View predicted protein structures via 3D-Beacons</strong> <br>
+ Jalview 2.11.2's <a href="features/structurechooser.html">Structure
+ Chooser includes a client for the 3D-Beacons Network</a>. Launched in
+ 2021, the 3D-Beacons network (<a
+ href="https://www.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/">www.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/</a>)
+ provides a central point for the retrieval of predicted and observed
+ 3D structures for sequences in Uniprot, including homology models
+ from Swiss-model and deep learning based predictions from the EBI's
+ Alphafold database (Orengo et al. 2020, <a
+ href="https://doi.org/10.12688/f1000research.20559.1">doi:10.12688/f1000research.20559.1</a>).<br>
</p>
+
<p>
- <em>JalviewJS News</em><br />With the release of Jalview 2.11.1.0,
- the team are now focused on bringing JalviewJS to full production.
- To follow our progress take a look at <em>http://www.jalview.org/jalview-js/</em>
- and follow updates on our new <a
- href="https://github.com/jalview/jalview-js/">JalviewJS
- Releases github repository</a>.
+ <strong>Support for viewing structures with ChimeraX and
+ Pymol</strong><br> Jalview's 3D structure viewer system has been
+ re-architected to allow easier integration of external structure
+ viewers, and takes advantage of the strucViz2 Chimera communications
+ library developed by Scooter Morris (<a
+ href="https://doi.org/10.1093/bioinformatics/btm329">doi:10.1093/bioinformatics/btm329</a>).<br /> <br />
+ The <a href="features/preferences.html#structure">Structures
+ Preferences tab</a> provides new options allowing ChimeraX and
+ Pymol to be used for visualising external 3D structures. Jalview
+ 2.11.2 has been tested with Pymol 2.5.0 (community) and 2.5.2
+ (incentive). For ChimeraX, we recommend using v1.3 or later.<br />Views
+ from all structure viewers are saved in Jalview Projects, allowing
+ them to be shared with others using Jalview 2.11.2 or later,
+ providing they have the same viewer installed and configured to be
+ used with Jalview.
</p>
+ <p>Other highlights include:</p>
+ <ul>
+ <li><strong>Easier configuration of <a
+ href="features/preferences.html#startup">Jalview's memory
+ allocation</a></strong></li>
+ <li>Import of annotated DNA and RNA loci via GenBank and EMBL
+ style flatfile</li>
+ <li>New <strong>command line launcher scripts</strong> (.sh, .ps1, .bat) usable on
+ macOS, Linux/Unix, Windows and documentation in Help
+ </li>
+
+
+
+
+ <p>
+ For the full release notes, see <a
+ href="releases.html#Jalview.2.11.2.0">the Jalview 2.11.2.0
+ release notes</a>.
+ </p>
+ <p>
+ <strong>Known Issues</strong>
+ </p>
+ <p></p>
+ </ul>
</body>
</html>
git://source.jalview.org / jalview.git / blobdiff