X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=3538ff4b1738f95e0516332b803c139306ed7206;hb=5115c19374566cc46eaac00f5ea0dbda5ff39b09;hp=04fcc6983b3836269a2dd43571edf3aa744404a3;hpb=11d7be472ca5ea89d69e5bb7882c0058b2c3c4b9;p=jalview.git diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html index 04fcc69..3538ff4 100755 --- a/help/html/whatsNew.html +++ b/help/html/whatsNew.html @@ -24,63 +24,48 @@

- What's new ? + 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.

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.

- Jalview 2.9 has been in development since December 2014. In addition - to a multitude of bug fixes and minor improvements (both small, and - rather big!), it also brings major new capabilities for codon-level - analysis of protein alignments and the retrieval and manipulation of - structural data.

For the full list of changes, see the - Jalview 2.9 Release Notes. + The full list of bugs fixed in this release can be found in the 2.11 Release Notes.

- Highlights in Jalview 2.9 + 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

Visualisation, editing and analysis of - cDNA and Protein alignments
A new Split View window allows linked - protein and nucleotide sequence alignments to be viewed, edited, - and analysed as one.
cDNA alignments can also be - reconstructed from protein alignments calculated by Jalview's web - services, and update in response to edits in the amino acid view.
To - start experimenting with cDNA/Protein analysis, jut drop a file - containing cDNA sequences which code for, and have IDs matching - proteins in an existing alignment, and Jalview will do the rest.
Enhanced Integration of UCSF Chimera
Jalview - 2.9 provides full support for the use of Chimera to view 3D - structures linked to alignment views in the Jalview Desktop. We've - also included support for saving Chimera sessions in Jalview - project files.
Jalview and Chimera communicate using local - web server connections, which may cause firewall alerts on some - systems, but has the advantage of allowing bidirectional - communication. Communication between Jalview and Chimera is now - much more responsive, and selected regions in Chimera are now - shown as highlighted regions in the Jalview desktop.
Interactive querying of the PDBe
Jalview - users can now browse and retrieve 3D structure data from the PDB - via the PDBe - Search API (Gutmanas - et al 2014). Developed in collaboration with the PDBe group at - EMBL-EBI, the interface allows both structured and free-text - queries to be performed, and allows automatic selection of the - most relevant structures for an alignment acording to a variety of - criteria.
Improved support for RNA visualisation
Jalview - 2.9 integrates the latest version of the VARNA RNA Viewer, and VARNA views - can also now be stored in Jalview projects. We've also dealt with - a number of lingering bugs in the VARNA/Jalview interface, - including the loss of pseudoknots when RNA secondary structure is - shown VARNA.
Protein Secondary Structure predictions - with JPred4Jalview includes a number of new features for working - with secondary structure predictions from the JPred4 server. These - include the ability to automatically hide insertions and highlight - mutations in an alignment with respect to a reference sequence. - Jalview 2.9's new scrollable SVG HTML export mode was also - developed specifically for the JPred4 server.
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