X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=3538ff4b1738f95e0516332b803c139306ed7206;hb=801c367379086cc38bf4d3059a8e30ca9f4e78c0;hp=448430d6afa3682fefa553af124b0750b0df2a49;hpb=448a82c6838c231172078210cfb1bdad138d4604;p=jalview.git diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html index 448430d..3538ff4 100755 --- a/help/html/whatsNew.html +++ b/help/html/whatsNew.html @@ -24,70 +24,48 @@

- What's new in Jalview 2.10.0b1 ? -

- Jalview 2.10.0b1 is a patch release for 2.10, the next major release - in the Jalview 2 series. Full details are in the Jalview 2.10b1 Release - Notes, but the highlights are below. + Jalview 2.11 - major and minor new features

Jalview 2.11 introduces support for loading VCF files, and new + filters and shading models for sequence features. Under the hood, + we've addressed many bugs, and also made some important changes in + the way the Jalview desktop is installed and launched.

Drag and drop reinstated for the Jalview desktop on - Windows, Linux and older OSX systems.
Problems loading local PDB files have been fixed
Conservation shading can be disabled for PID and consensus - based colour scheme
VCF Support. Proteins and genomic contigs with + chromosomal location annotation (such as protein coding genes + retrieved from Ensembl) can be annotated with variants imported + from a local VCF file.
The Jalview Launcher and Update System
+ Jalview's new installation model means you'll only need to + download and install Jalview once. After installation, Jalview + will automatically keep itself up to date. The launcher also sets + Jalview's memory automatically, so you'll never again have to + manually configure Java's memory settings.
We are grateful to + Install4J who provided us with a free license for their + installation system, and Jalview's over the air update system is + via Getdown.

Major highlights of the 2.10.0 Release

+ The full list of bugs fixed in this release can be found in the 2.11 Release Notes. +

+ Jalview and Java 11, 13, and onwards +

Java 11 provides improved performance and better OS + integration, so we now recommend users select our Java 11 Jalview + distribution rather than the legacy Java 8 build.

+ Known Issues - update for 211

Ensembl sequence fetcher
Annotated - Genes, transcripts and proteins can be retrieved via Jalview's new - Ensembl REST - client. Support for import of Ensembl data allows: -
- Aligned locus view
  Transcripts - retrieved for a gene identifier via the Ensembl or - EnsemblGenomes sequence databases are automatically aligned to - their reference genome, and introns hidden from the view.
- Sequence variant data
  Jalview - propagates variant annotation on genomic regions onto - transcripts and protein products, complete with associated - metadata such as clinical significance.
Ensembl and ENA 'show cross-references' - support
The Calculations menu's 'Show - cross-references' now offers Ensembl as well as EMBLCDS and - Uniprot when CDS/Protein mapping data is available for download or - display. This allows variant annotation to be added directly to an - alignment of UniProt sequences.
Working with structures -
- More accurate structure mappings
  - Jalview now utilises the PDBe's SIFTS database (at EMBL-EBI) - to match structures - to UniProt sequences, even for structures containing - multiple copies of a sequence.
- Import structures as mmCIF
  Jalview - now downloads data from the EMBL-EBI's PDBe site as mmCIF. This allows very large - structures to be imported, such as the HIV virus capsid - assembly.
- Chimera users will need to upgrade to - 1.11.1
  If you use Chimera to view structures - downloaded by Jalview 2.10, you will need to make sure you are - running the latest version of Chimera.
UniProt Free Text Search
The new - search dialog for UniProt allows you to browse and retrieve - sequences with free-text search, or structured queries.
Reference sequence alignment view
- Jalview 2.9 introduced support for reference sequences. In 2.10, - when a reference sequence is defined for the alignment, the - alignment column ruler is now numbered according to the reference - sequence. The reference sequence for alignment views can also be - saved and restored from Jalview projects.
OSX: The 'Open File' dialog for Jalview's Groovy Console + appears with the title 'Save As', and attempting to select a file + to load yields a FileNotFound exception.
The workaround is to first + clear the 'Untitled' filename before selecting the file you wish + to load. +
OSX: Links don't open when clicked on or via the Sequence + or Alignment window popup menu.
OSX (Webstart): JalviewÂ only displays old news feed items