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Jalview provides patches for critical bugs affecting the Find function, and analysis of linked CDS and Protein alignments.

Issues Resolved

  • Find doesn’t always highlight all matching positions in a sequence (bug introduced in
  • Alignments containing one or more protein sequences can be classed as nucleotide
  • CDS alignment doesn’t match original CDS sequences after alignment of protein products (known defect first reported for
  • No tooltip or popup menu for genomic features outwith CDS shown overlaid on protein
  • Overlapping CDS in ENA accessions are not correctly mapped by Jalview (e.g. affects viral CDS with ribosomal slippage, since 2.9.0)
  • Spliced transcript CDS sequences don’t show CDS features
  • Selections in CDS sequence panel don’t always select corresponding protein sequences
  • Make groups from selection for a column selection doesn’t always ignore hidden columns


  • Space character in Jalview install path on Windows prevents install4j launching getdown


  • Fixed typos and specified compatible gradle version numbers in doc/building.md