</head>
<body>
<p>
- <strong>Jalview 2.10.2b1 bugfix release</strong>
+ <strong>What's new in Jalview 2.10.3 ?</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 about the bugs addressed. This release 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
+ Version 2.10.3 is due for release in October 2017. The full list of
+ bug fixes and new features can be found in the <a
+ href="releases.html#Jalview.2.10.3"> 2.10.3 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- calculating PCA and different types of tree have been replaced by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>
git://source.jalview.org / jalview.git / commitdiff