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 based on Three Rings' Getdown system.
• Backup files
  Jalview will automatically create backups when overwriting existing files, and - unlike with earlier versions, should Jalview crash during a save, the original file will be unaffected.
• PCA plots stored in Jalview Projects
  The PCA viewer has also been enhanced and the user interface revised.

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

The Jalview application comes bundled with its own independent Java installation which will be updated automatically from www.jalview.org. Version 2.11.0 includes an AdoptOpenJDK Java 1.8 runtime, but installations will be migrated to the latest Java release once remaining issues have been addressed.