X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=0abd2a7b9501e9f1fffc3bc4456f39ec4af1d50a;hb=b8790847f686f6d31d2098c6b9804f8acc1041c9;hp=8a0436dd0e6c35df296aefaed837cf04b8ff0f65;hpb=ce6edf5c9421ce38f625886885ed2cd8f506f08d;p=jalview.git
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- What's new in Jalview 2.10.2 ?
+ What's new in Jalview 2.10.4 ?
- Full details about Jalview 2.10.2 are in the Release Notes, but the
- highlights are below.
+ This is the May 2018 release of Jalview, and the last in the 2.10.x series. Jalview 2.10.4 includes:
- - New UI, and faster and more configurable implementation for PCA, Neighbour-Joining and UPGMA Trees
- Menu entries for calculating PCA and different types of tree have
- been replaced by a single Calculations dialog box. The
- underlying implementation for the PCA and tree calculations have been
- made faster and more memory efficient. A new framework has also been
- created for the score models used to calculate distances between
- sequences. This framework allows import of substitution matrices in
- NCBI and AAIndex format, and custom score models to be created via a
- groovy script.
- - Update to JABAWS 2.2
Jalview's
- alignment, protein conservation analysis, and protein disorder and
- RNA secondary structure prediction services are now provided by JABAWS 2.2.
- Several of the programs provided as services have been updated, so
- their options and parameters have changed.
- - New preferences for opening
- web pages for database cross-references via the UK Elixir's
- EMBL-EBI's MIRIAM database and identifiers.org services.
-
- - Showing and hiding regions
-
- - Hide
- insertions 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.
-
+ - Numerous efficiency improvements in the renderer and overview when working with large alignments with lots of hidden columns
+ - Use of HTTPS when connecting to Uniprot, Ensembl and other EBI web services
+ - Critical patches for running Jalview on OSX with Java 10
+ - Easier adjustment of the Alignment ID panel and Annotation panel
+ - Improved support for mapping between 3D Structures and Uniprot Protein Sequences
+ - Improved support for discovering CDS and transcripts for Proteins and Ensembl gene IDs
+ - New buttons on the Structure Chooser for adding structures
+ to an existing view, and disabling automatic superposition
+ according to linked alignments
+ - Annotation transfer between Chimera and Jalview (formerly only
+ available in 'Experimental' mode)
- Experimental Features
+ The full list of bugs fixed in this release can be found in the 2.10.4
+ Release Notes.
-
- This release of Jalview includes a new option in the Jalview Desktop
- that allows you to try out features that are still in development.
- To access the features described below, please first enable the Tools→Enable
- Experimental Features option, and then restart Jalview.
-
-