Version 2.5

Thank you to everyone who wrote letters of support last year for our application to the BBSRC, we should hear the outcome in the next couple of months.

We are now applying to the Wellcome Trust to renew funding to support Jalview's use in biomedical sequence analysis, including interpretation of genomic variation and long read RNA data (e.g. Nanopore) at the protein coding level. If you would like Jalview to continue to develop and be supported then please take a few minutes to write us a support letter saying how you use Jalview in your research/teaching.

Write as a PDF including your institution's heading and send to: by Friday 22nd March 2019.

Thank you!

Version Date: 

New Features

New Capabilities

  • URL links generated from description line for regular-expression based URL links (applet and application)
  • Non-positional feature URL links are shown in link menu
  • Linked viewing of nucleic acid sequences and structures
  • Automatic Scrolling option in View menu to display the currently highlighted region of an alignment.
  • Order an alignment by sequence length, or using the average score or total feature count for each sequence.
  • Shading features by score or associated description
  • Subdivide alignment and groups based on identity of selected subsequence (Make Groups from Selection).
  • New hide/show options including Shift+Control+H to hide everything but the currently selected region.


  • Fetch DB References capabilities and UI expanded to support retrieval from DAS sequence sources
  • Local DAS Sequence sources can be added via the command line or via the Add local source dialog box.
  • DAS Dbref and DbxRef feature types are parsed as database references and protein_name is parsed as description line (BioSapiens terms).
  • Enable or disable non-positional feature and database references in sequence ID tooltip from View menu in application.
  • Group-associated consensus, sequence logos and conservation plots
  • Symbol distributions for each column can be exported and visualized as sequence logos
  • Optionally scale multi-character column labels to fit within each column of annotation row
  • Optional automatic sort of associated alignment view when a new tree is opened.
  • Jalview Java Console
  • Better placement of desktop window when moving between different screens.
  • New preference items for sequence ID tooltip and consensus annotation
  • Client to submit sequences and IDs to Envision2 Workflows
  • Vamsas Capabilities
    • Improved VAMSAS synchronization (jalview archive used to preserve views, structures, and tree display settings)
    • Import of vamsas documents from disk or URL via command line
    • Sharing of selected regions between views and with other VAMSAS applications (Experimental feature!)
    • Updated API to VAMSAS version 0.2


  • Middle button resizes annotation row height
  • New Parameters
    • sortByTree (true/false) - automatically sort the associated alignment view by the tree when a new tree is opened.
    • showTreeBootstraps (true/false) - show or hide branch bootstraps (default is to show them if available)
    • showTreeDistances (true/false) - show or hide branch lengths (default is to show them if available)
    • showUnlinkedTreeNodes (true/false) - indicate if unassociated nodes should be highlighted in the tree view
    • heightScale and widthScale (1.0 or more) - increase the height or width of a cell in the alignment grid relative to the current font size.
  • Non-positional features displayed in sequence ID tooltip


  • Features format: graduated colour definitions and specification of feature scores
  • Alignment Annotations format: new keywords for group associated annotation (GROUP_REF) and annotation row display properties (ROW_PROPERTIES)
  • XML formats extended to support graduated feature colourschemes, group associated annotation, and profile visualization settings.

Issues Resolved

  • Source field in GFF files parsed as feature source rather than description
  • Non-positional features are now included in sequence feature and gff files (controlled via non-positional feature visibility in tooltip).
  • URL links generated for all feature links (bugfix)
  • Added URL embedding instructions to features file documentation.
  • Codons containing ambiguous nucleotides translated as 'X' in peptide product
  • Match case switch in find dialog box works for both sequence ID and sequence string and query strings do not have to be in upper case to match case-insensitively.
  • AMSA files only contain first column of multi-character column annotation labels
  • Jalview Annotation File generation/parsing consistent with documentation (e.g. Stockholm annotation can be exported and re-imported)
  • PDB files without embedded PDB IDs given a friendly name
  • Find incrementally searches ID string matches as well as subsequence matches, and correctly reports total number of both.
  • Application:
    • Better handling of exceptions during sequence retrieval
    • Dasobert generated non-positional feature URL link text excludes the start_end suffix
    • DAS feature and source retrieval buttons disabled when fetch or registry operations in progress.
    • PDB files retrieved from URLs are cached properly
    • Sequence description lines properly shared via VAMSAS
    • Sequence fetcher fetches multiple records for all data sources
    • Ensured that command line das feature retrieval completes before alignment figures are generated.
    • Reduced time taken when opening file browser for first time.
    • isAligned check prior to calculating tree, PCA or submitting an MSA to JNet now excludes hidden sequences.
    • User defined group colours properly recovered from Jalview projects.