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<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * 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 2.8.1 includes new features for group creation, RNA secondary
- structure prediction and a host bug fixes. It also includes support
- for <a href="http://www.compbio.dundee.ac.uk/JABAWS">version 2.1
- of JABA</a> and includes a Spanish translation of its user interface.<br />
- The highlights are detailed below, and the full list is given in the <a
- href="releases.html#Jalview2.8.1">Jalview 2.8.1 Release Notes</a>.
- </p>
- <p>The Desktop and web based applet include new keystrokes for
- defining and undefining groups, and PAM250 has been added to the range
- of score models available for use by the tree and PCA calculations.
- The Jalview project file format has also been extended for handling
- RNA and protein secondary structure annotation, in anticipation for
- new structure based secondary structure support in Jalview 2.8.2.</p>
- <p><strong>Internationalisation</strong></p>
- <p>Jalview 2.8.1 is the first release to include support for
- displaying Jalview's user interface in different languages. In August
- 2013, David Roldán-Martinez took on the task of
- internationalising Jalview's user interface. He also recruited Sara
- Hernández Díaz and Laura Ferrandis Martinez who created
- Jalview's first spanish user interface translation.</p>
- <p>
- If you notice any problems, or would like to help translate Jalview's
- user interface into other languages, head over to <a
- href="http://issues.jalview.org">issues.jalview.org</a> and put in a
- feature request describing the translations you can provide to the <a
- href="http://issues.jalview.org/browse/JAL/component/10682">i18n
- component</a>. David has also <a
- href="https://wiki.jalview.org/index.php/Development:i18n">documented
- the process of creating i18n translations</a> to help you get started.
- </p>
- <p><strong>RNA Secondary Structure Prediction with JABA 2.1</strong></p>
- <p>
- This version of Jalview includes a client to access the new services available in <a
- href="http://www.compbio.dundee.ac.uk/jabaws/">JABA v2.1</a> , which
- provides services for RNA consensus secondary structure prediction and
- two new alignment programs (<a
- href="http://sourceforge.net/projects/glprobs/">GLProbs</a> and <a
- href="http://sourceforge.net/projects/msaprobs/">MSAProbs</a>).</p>
- <p>
- To see how to perform RNA secondary structure predictions like the one below, take a look at the <a href="webServices/RNAalifold.html">RNAAliFold
- client documentation</a>.
- </p>
- <div align="center">
- <img src="webServices/RNAalifoldAnnotationRows.png" width="500" height="216"> <br> <em>The RNAalifold client was implemented by Jalview's 2013
- summer student, Dan Barton.</em>
- </div>
+ <p>
+ <strong>Jalview 2.10.2b1 bugfix release</strong>
+ </p>
+ <p>
+ This is patch release for 2.10.2. See the <a
+ href="releases.html#Jalview.2.10.2b1">release notes</a>.
+ </p>
+ <ul>
+ <li>Gaps are now rendered as dark grey in overview window</li>
+ </ul>
+ <p>
+ <strong>What's new in Jalview 2.10.2 ?</strong>
+ </p>
+ <p>
+ Version 2.10.2 was released in August 2017, and introduced new user
+ interface features, improved and more extensible tree and PCA
+ analysis, more robust 3D structure viewing with UCSF Chimera and an
+ updated service client for JABAWS. The full list of bug fixes and
+ new features can be found in the <a
+ href="releases.html#Jalview.2.10.2"> 2.10.2 Release Notes</a>, but
+ the highlights are below.
+ </p>
+ <ul>
+ <li><strong>New dialog and faster and more
+ configurable Tree and PCA calculations</strong><br> Menu entries for
+ calculating PCA and different types of tree have been replaced by
+ a single <a href="calculations/calculations.html"><em>Calculations</em>
+ dialog box</a>. The underlying implementation for the PCA and tree
+ calculations have been made faster and more memory efficient.</li>
+ <li><strong>Extensible score models</strong><br />A new
+ framework has also been created for the score models used to
+ calculate distances between sequences and shade alignments. This
+ framework allows import of substitution matrices in NCBI and
+ AAIndex format.<br /> <strong>PCA Bug Fixes</strong>. Jalview's
+ implementation of PCA differed in its treatment of gaps and
+ non-standard residues. The BLOSUM62 matrix also included a typo
+ that affected results. See the <a
+ href="releases.html#2102scoremodelbugs">2.10.2 release note
+ about score model bugs</a> for details and how to reinstate legacy
+ behaviour.</li>
+ <li><strong>Update to JABAWS 2.2</strong><br />Jalview's
+ alignment, protein conservation analysis, and protein disorder and
+ RNA secondary structure prediction services are now provided by <a
+ href="http://www.compbio.dundee.ac.uk/jabaws">JABAWS 2.2</a>.
+ Several of the programs provided as JABAWS 2.2 services have been
+ updated, so their options and parameters have changed.</li>
+ <li><strong>URL linkouts to other bioinformatics
+ databases</strong><br />New preferences for <a
+ href="webServices/urllinks.html">opening web pages for
+ database cross-references</a> via the UK Elixir's EMBL-EBI's MIRIAM
+ database and identifiers.org services.</li>
+ <li><strong>Showing and hiding regions</strong> <br /> <a
+ href="menus/popupMenu.html#hideinserts">Hide insertions</a> in the
+ PopUp menu has changed its behaviour. Prior to 2.10.2, columns
+ were only shown or hidden according to gaps in the sequence under
+ the popup menu. Now, only columns that are gapped in all selected
+ sequences as well as the sequence under the popup menu are hidden,
+ and column visibility outside the selected region is left as is.
+ This makes it easy to filter insertions from the alignment view
+ (just select the region containing insertions to remove) without
+ affecting the rest of the hidden columns.</li>
+ <li><strong>Gap count - a.k.a. the Occupancy
+ Annotation Row</strong><br /> Another way to filter columns according to
+ the presence of gaps is to enable the <strong>Occupancy
+ Annotation</strong> row via Jalview's Preferences. This annotation row
+ shows a histogram of the number of aligned residues at each
+ column. The <a href="features/columnFilterByAnnotation.html">Select
+ By Annotation</a> dialog now also includes a percentage threshold
+ mode, to make it easy to filter alignments to show only those
+ columns with a particular fraction of aligned sequences.</li>
+ <li><strong>Recent search history for Find, PDBe and
+ Uniprot</strong><br />Easily repeat a previous search for <a
+ href="features/search.html#queryhistory">Find</a> and the free
+ text search system (for querying Uniprot and the PDBe).</li>
+ <li><strong>Improved Overview Window</strong><br />The <a
+ href="features/overview.html">alignment overview</a> is now easier
+ to use when working with alignments of more than 5000 rows and
+ columns, and features a new pop-up menu that allows hidden regions
+ to be excluded from the overview. It also works with CDS/Protein
+ alignments and MSA views in wrapped mode.</li>
+ <li><strong>3D Structure</strong><br />Jalview's communication
+ with UCSF Chimera has been made more robust, particularly when
+ working with many structures and long sequences. Regions in
+ structures that correspond to hidden regions in an alignment view
+ are now left un-coloured, making it easier to highlight specific
+ features in 3D. See below for <a href="#experimental">experimental
+ features for exchanging annotation between Chimera and Jalview.</a></li>
+ </ul>
+ <p>
+ <strong>Scripting</strong><br />New <a
+ href="http://www.jalview.org/examples/groovy">groovy examples</a>
+ demonstrate Jalview 2.10.2 APIs for creation of data-driven
+ colourschemes, and custom alignment file handlers. The <a
+ href="groovy/featuresCounter.html">FeatureAnnotationWorker</a>
+ introduced in Jalview 2.10 has also been refactored to allow
+ efficient counting across multiple feature types. Please be aware
+ that feature counter scripts created for earlier versions will not
+ execute in Jalview 2.10.2.
+ </p>
+ <p>
+ <strong><a name="experimental">Experimental Features</a></strong>
+ </p>
+ <p>
+ This release of Jalview introduces an <em>Experimental Features</em>
+ option in the Jalview Desktop's <em>Tools</em> menu that allows you
+ to try out features that are still in development. To access the
+ experimental features below - first enable the <strong>Tools→Enable
+ Experimental Features</strong> option, and then restart Jalview.
+ </p>
+ <ul>
+ <li><em>Annotation transfer between Chimera and Jalview</em><br />Two
+ <a href="features/chimera.html#experimental">new entries in
+ the Chimera viewer's Chimera menu</a> allow positional annotation to
+ be exchanged between Chimera and Jalview.</li>
+ </ul>
+
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