- <p>
- <strong>What's new ?</strong>
- </p>
- <p>Jalview 2.8 includes a brand new logo, which you'll see in file
- browsers, splash screens, and also on the new look Jalview site.</p>
- <p>
- In addition to our new look, Jalview 2.8 includes a number of new
- features.. some of which have been in development since July 2010. The
- highlights are below, and - as usual, for a comprehensive list, take a
- look at the <a href="releases.html#Jalview2.8">Jalview 2.8 Release
- Notes</a>.
- </p>
- <p>
- <strong>Highlights in Jalview Version 2.8</strong>
- </p>
- <ul>
- <li>Improved JABA client and new JABAWS 2.0 Services
- <ul>
- <li>AACon alignment conservation</li>
- <li>Protein disorder - DisEMBL, RONN, GlobPlot and IUPred</li>
- <li>Clustal Omega - huge protein alignments</li>
- </ul>
- </li>
- <li><strong>Support for RNA</strong>
- <ul>
- <li>Import sequence and alignment associated WUSS or VIENNA
- secondary structure notation from stockholm and clustalW files or
- as jalview annotation.</li>
- <li>Interactive editing of RNA secondary structure annotation</li>
- <li>Colour scheme for purine/pyrimidine and to highlight RNA
- helices</li>
- <li>RNA canonical base pair consensus score and sequence logo</li>
- <li>Embedded <a href="http://varna.lri.fr/">VARNA</a> RNA
- secondary structure viewer in the Desktop
- </li>
- </ul> See <a href="na/index.html">Nucleic Acid Support</a> for full
- details.</li>
- <li>Parse and display T-COFFEE alignment quality scores</li>
- <li>Shade individual sequence positions according to alignment
- annotation scores</li>
- <li>Enhanced PCA viewer: more export options, and switch between
- different PCA modes and residue score models</li>
- <li>New Jalview Desktop database fetcher GUI</li>
- <li>Support for DAS 1.6 and DAS 2.0 sources</li>
- <li>Export sequence database annotation as HTML report</li>
- <li>Normalised Sequence Logo Display</li>
- </ul>
- <p>
- <strong>Issues Resolved (a select list - see the <a
- href="releases.html#Jalview2.8">release history</a> for full details)
- </strong>
- </p>
- <p>
- <strong>Issues in the Jalview Desktop</strong>
- <ul>
- <li>PDB, Unprot and EMBL (ENA) databases retrieved via wsdbfetch
- REST service<!--<a href='http://issues.jalview.org/browse/JAL-636'>JAL-636</a>-->
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-368'>JAL-368</a>] - -->
- <!--[<a href='http://issues.jalview.org/browse/JAL-153'>JAL-153</a>] - -->Stop
- windows being moved outside desktop on OSX
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-758'>JAL-758</a>] - -->Filetype
- associations not installed for webstart launch
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-849'>JAL-849</a>] - -->Jalview
- does not always retrieve progress of a JABAWS job execution in full
- once it is complete
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-983'>JAL-983</a>] - -->View
- all structures superposed fails with exception
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-994'>JAL-994</a>] - -->Jnet
- job queues forever if a very short sequence is submitted for
- prediction
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1022'>JAL-1022</a>] - -->Structure
- view highlighting doesn't work on windows 7
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1026'>JAL-1026</a>] - -->Jalview
- desktop fails to launch with exception when using proxy
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1031'>JAL-1031</a>] - -->Tree
- calculation reports 'you must have 2 or more sequences
- selected' when selection is empty
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1062'>JAL-1062</a>] - -->DAS
- Sequence retrieval with range qualification results in sequence xref
- which includes range qualification
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1111'>JAL-1111</a>] - -->Cannot
- close news reader when JABAWS server warning dialog is shown
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1131'>JAL-1131</a>] - -->Edited
- sequence not submitted to web service
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1134'>JAL-1134</a>] - -->Jalview
- 2.7 Webstart and InstallAnywhere installer doesn't unpack and run
- on OSX Mountain Lion
- <ul>
- <li>The workaround for webstart is to go into the Security
- panel (gatekeeper symbol) under System settings, and select the
- 'allow any code to run' setting.</li>
- </ul>
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1144'>JAL-1144</a>] - -->Annotation
- panel not given a scroll bar when sequences with alignment annotation
- are pasted into the alignment
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1148'>JAL-1148</a>] - -->Sequence
- associated annotation rows not associated when loaded from jalview
- project
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1145'>JAL-1145</a>] - -->Exceptions
- when copy/paste sequences with grouped annotation rows to new window
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1149'>JAL-1149</a>] - -->Browser
- launch fails with NPE on java 1.7
- </li>
+ <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> for full
+ details bugs addressed in this version, which also introduces
+ additional improvements to the overview panel, and patches for
+ several minor issues including the ability to correctly recover
+ cross-references for Uniprot protein sequences from Ensembl.
+ </p>
+ <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>