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.

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.

• 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): Jalview only displays old news feed items