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. A Java 11 based installation is available from the Jalview development pages. ![]() Version 2.11.0 includes an AdoptOpenJDK Java 1.8 runtime which will be kept up to date. The Jalview application comes bundled with its own independent Java installation. The full list of bugs fixed in this release can be found in the 2.11 Release Notes. The Backups tab in Jalview’s preferences dialog allows the number and format of backup filenames to be configured. 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 PCA viewer user interface has also been improved.īackup files. The Translate as cDNA option now offers alternative amino acid coding schemes. Jalview’s sequence feature datamodel has also been further optimised, and is now maintained as a separate library IntervalStoreJ (available at )Īlternative tables for CDS translation. 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. 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.įeature filters and attribute colourschemes. 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. The launcher also sets Jalview’s memory automatically, so you’ll never again have to manually configure Java’s memory settings. ![]() ![]() After installation, Jalview will automatically keep itself up to date. Jalview’s new installation model means you’ll only need to download and install Jalview once. Under the hood, we’ve addressed many bugs, and also made some important changes in the way the Jalview desktop isinstalled and launched. This major release introduces support for loading VCF files, and new filters and shading models for sequence features. We are quite excited about the release of Jalview 2.11.0!
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