Jalview update! 2.8.0b1 Released

Jalview 2.8.0b1 is a bugfix release for Jalview version 2.8.

This bug fix release includes numerous minor enhancements made over the last 12 months. Importantly, it is also the first release that provides Jalview as a trusted application, signed with a certificate donated to us by Certum. As usual you can find the comprehensive list in the Jalview 2.8.0b1 Release Notes.

Enhancements and new features

  • Allow disorder predictions to be made on the current selection (or visible selection) in the same way that JPred works
  • allow import of data from gzipped files
  • Improved per-sequence ‘colour-by-annotation’ performance
  • Support ‘’ style escaping of quotes in Newick files
  • group options for JABAWS service by command line name
  • Select primary source when selecting authority in database fetcher GUI
  • COMBINE statement uses current SEQUENCE_REF and GROUP_REF scope to group annotation rows
  • add .mfa to FASTA file extensions recognised by Jalview
  • groovy scripting for headless jalview operation
  • Output in Stockholm format

Bug fixes

  • Uniprot and PDB database cross-reference fetching works properly
  • ‘View all structures’ in the desktop is more reliable
  • Web services parameter dialog box shows the options enabled for different presets
  • Interactive creation of RNA secondary structure works more smoothly
  • Keyboard mode ‘P’ command jumps to the right place
  • Improved support for parsing database cross-references via Stockholm and Rfam database
  • Improved semantics in annotation files for grouping annotation rows associated with particular sequences and groups
  • More robust DNA->Amino acid translation
  • Improved Headless-mode operation for DAS annotation retrieval, groovy script execution and alignment figure generation
  • annotation label tooltip text needs to be wrapped