<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * Copyright (C) 2014 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.
*
<title>What's new ?</title>
</head>
<body>
- <p>
- <strong>What's new ?</strong>
- </p>
- <p>
- Jalview 2.8.2 is the first release produced by our new core
- development team.<br /> It incorporates many minor improvements and
- bug-fixes, and new features for working with 3D structure data,
- shading alignments by secondary structure and generation of alignment
- figures as Scalable Vector Graphics. <br />The majority of
- improvements in this version of Jalview concern the desktop
- application. As ever, the highlights are detailed below,
- and the full list is given in the <a
- href="releases.html#Jalview.2.8.2">Jalview 2.8.2 Release Notes</a>.
- </p>
- <p>
- <strong>Annotation visualisation</strong> <br /> The alignment window
- includes a new <em>Annotations</em> menu which provides controls for
- the layout and display of sequence, group and alignment associated
- annotation rows. It also now includes the <em>Autocalculated
- Annotation</em> submenu (formerly located in the View menu), which
- includes settings for the calculation and display of sequence
- consensus, logos, and amino acid conservation for the alignment and
- subgroups.
- </p>
- <p>
- <strong>Sequence associated annotation</strong><br /> New controls
- have also been added to the Sequence ID popup menu for the propagation
- and display of sequence associated annotation such as secondary
- structure assignments and disorder predictions. Annotation associated
- with one or a group of sequence already shown on the alignment may be
- shown or hidden, and any available annotation from 3D structure or
- calculations performed in other Jalview windows can be copied to the
- alignment
- <em>via</em> the <strong>Add Reference Annotation</strong> option.<br />
- The <strong>Colour by annotation</strong> function has also been
- improved, allowing secondary structure annotation to be used to shade
- sequences and alignment columns. Protein sequences can be coloured
- according to the presence of a helix or sheet at each position, and
- RNA sequences can be shaded according to each structure's stem/helix
- pattern - which enables different RNA folding topologies to be quickly
- identified.
- </p>
- <p>
- <strong>3D Structural data analysis and display</strong><br />
- Jalview now employs Jmol's PDB data API to retrieve secondary
- structure assignments made by the DSSP algorithm. It can also employ
- web services to obtain secondary structure assignments from RNA
- structures. These assignments are shown as sequence associated
- annotation for sequences which have cross-references to the PDB, or
- have had PDB files associated with them via the <em>Structures</em>
- submenu of the sequence ID popup menu. The extraction and display of
- secondary structure and B-factor column annotation is controlled <em>via</em>
- a new <strong>Structure</strong> tab in the Jalview Desktop's
- Preferences dialog box.
- </p>
- <p>
- <Strong>Interoperation with UCSF Chimera</Strong><br /> The desktop
- application can now be configured to employ UCSF Chimera for the
- display of 3D structure data. UCSF Chimera is a python-based
- high-performance molecular graphics and animation system developed by
- the Resource for Biocomputing, Visualisation, and Informatics at the
- University of California.<br />Jalview employs the 'StructureViz'
- communication mechanism developed for Cytoscape by Morris et al.
- (http://www.ncbi.nlm.nih.gov/pubmed/17623706) in 2007. This mechanism
- allows Jalview to send commands to Chimera, enabling structures to be
- superimposed and shaded according to associated multiple aligmment
- views. <br />Support for Chimera in Jalview 2.8.2 is experimental, and we
- would appreciate feedback ! Please send your comments to
- jalview-discuss@jalview.org, and keep up to date with this feature's
- development via http://issues.jalview.org/browse/JAL-1333.
- </p>
- <p>
- <strong>Export of alignment figures as Scalable Vector
- Graphics</strong> <br />Scalable Vector Graphics (SVG) files are now widely
- supported by web browsers and graphics design programs, and allow
- high-quality graphics for interactive exploration and publication.
- Jalview now supports the generation of SVGs interactively (via the
- Export) menu, and from the command line for server-side figure
- generation.
- </p>
-
+ <p>
+ <strong>What's new in Jalview 2.10.4 ?</strong>
+ </p>
+ <p>
+ This is the May 2018 release of Jalview, and the last in the 2.10.x series. Jalview 2.10.4 includes:
+ </p>
+ <ul>
+ <li>Numerous efficiency improvements in the renderer and overview when working with large alignments with lots of hidden columns</li>
+ <li>Use of HTTPS when connecting to Uniprot, Ensembl and other EBI web services</li>
+ <li>Critical patches for running Jalview on OSX with Java 10</li>
+ <li>Easier adjustment of the Alignment ID panel and Annotation panel</li>
+ <li>Improved support for mapping between 3D Structures and Uniprot Protein Sequences</li>
+ <li>Improved support for discovering CDS and transcripts for Proteins and Ensembl gene IDs</li>
+ <li>New buttons on the Structure Chooser for adding structures
+ to an existing view, and disabling automatic superposition
+ according to linked alignments</li>
+ <li>Annotation transfer between Chimera and Jalview <em>(formerly only
+ available in 'Experimental' mode)</em></li>
+ </ul>
+ <p>
+ The full list of bugs fixed in this release can be found in the <a href="releases.html#Jalview.2.10.4">2.10.4
+ Release Notes</a>.
+ </p>
</body>
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