We are quite excited about the release of Jalview 2.11.0!
This major release 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 isinstalled and launched.
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 ej Technologies for providing a free open source project license for install4j, and also to Three Rings Design for Jalview’s new over the air update system: Getdown.
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.
Feature filters and attribute colourschemes. A new Feature Display Settings dialog allows filters and feature attribute based colourschemes to be constructed, and a new filters column added to the Feature Settings dialog. Jalview’s sequence feature datamodel has also been further optimised, and is now maintained as a separate library IntervalStoreJ (available at GitHub - bartongroup/IntervalStoreJ: A read-write Java implementation of NCList for efficient lookup of overlapping intervals)
Alternative tables for CDS translation. The Translate as cDNA option now offers alternative amino acid coding schemes.
PCA plots stored in Jalview Projects. The PCA viewer user interface has also been improved.
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. The Backups tab in Jalview’s preferences dialog allows the number and format of backup filenames to be configured.
The full list of bugs fixed in this release can be found in the 2.11 Release Notes.
Jalview and Java 11, and onwards
The Jalview application comes bundled with its own independent Java installation. Version 2.11.0 includes an AdoptOpenJDK Java 1.8 runtime which will be kept up to date. A Java 11 based installation is available from the Jalview development pages.
Long time Jalview users will notice that this release no longer features the Vamsas desktop menu, or a Distributed Annotation System (DAS) tab on the feature settings dialog. DAS is no longer supported by major bioinformatics databases, and we decided that it was no longer feasible to maintain either JDAS or the VAMSAS client library which rely on out-dated Java XML binding technologies.
Visit the JalviewJS webpage to find out more, and to open JalviewJS in a web browser (Chrome or Firefox recommended).
Best wishes for 4th of July from Jim, Ben, Suzanne, Mungo, Geoff and also Bob!