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Welcome to the Jalview project's issue tracker.
If you experience any problems, please contact James (Jim) Procter.

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  1. Improvement JAL-4543
    Enable column selection on line graph annotations
  2. Improvement JAL-4542
    Selection of Sequences in Sequence Panel Does Not Highlight Corresponding Nodes in Secondary Structure Similarity Tree
  3. Bug JAL-4540
    Tree calculation out of memory error not passed to user!
  4. Bug JAL-4539
    find causes stack overflow
  5. Improvement JAL-4538
    Select/Hide/Highlight columns or sequence positions by per-sequence annotation
  6. Bug JAL-4537
    Tree node labels incorrectly appear grey when a tree is first created
  7. Task JAL-4531
    Release 2.11.5.0
  8. Improvement JAL-4530
    Add an Applescript .app to the DMG to allow easy installation to ~/Applications folder and optionally add Jalview to the Dock
  9. Improvement JAL-4528
    Allow calculation of annotation track based trees involving just one or two sequences
  10. Improvement JAL-4527
    Allow secondary structure rows with 'PROVIDER' metadata to be exported and imported as Jalview annotations file
  11. Improvement JAL-4526
    Update jalview webservices documentation page
  12. Bug JAL-4523
    Loading progress bar remains visible indefinitely for some structures in SIMSApiper data
  13. Improvement JAL-4521
    allow trees/PCA for secondary structures when just one sequence is shown in algiment
  14. Improvement JAL-4520
    sensible precision for tree distance labels
  15. Task JAL-4517
    store and restore trees linked to annotation rows in Jalview projects
  16. Bug JAL-4516
    Resizing an alignment window from the top can completely obscure sequences and annotation divider
  17. Improvement JAL-4515
    Add Coloured Backgrounds for Grouped Nodes in Similarity Tree
  18. Bug JAL-4514
    Residue highlighting in pymol not working in 3.0.4
  19. Improvement JAL-4513
    Consistent colours assigned to groups generated when subdividing tree
  20. Improvement JAL-4509
    Assign perceptually distinct colours for secondary structure providers
  21. Bug JAL-4507
    Exported Consensus annotation then loads (Load Features/Annotations) as a Pfam file sequence onto the alignment
  22. Bug JAL-4505
    install4j installation wizard looks bad in dark mode
  23. Bug JAL-4500
    Update flatlaf for more OS visual integration
  24. Improvement JAL-4494
    Migrate to Java 11 for Jalview production version
  25. New Feature JAL-4489
    automatic clustering of sequences using distance matrices
  26. Epic JAL-4488
    routine service and program integration tests
  27. Bug JAL-4486
    secondary structure annotation not mapped correctly to sequence for some structures
  28. Improvement JAL-4484
    Temporarily configure 3d structure viewer via CLI for a jalview session
  29. Bug JAL-4477
    CAN'T INSTALL Jalview
  30. Improvement JAL-4476
    Reformat Secondary Structure Consensus Annotation Labels
  31. Bug JAL-4472
    jalview --version or other command line output include misleading 'Version: TEST' information
  32. Improvement JAL-4466
    allow pairwise alignment gap parameters to be adjusted
  33. Bug JAL-4464
    cannot store/restore group associated secondary structure consensus annotations
  34. Story JAL-4463
    Importing lots of sequences and structures example
  35. Bug JAL-4437
    An app for a particular getdown channel can't launch builds from other channels due to failed background image downloads
  36. New Feature JAL-4436
    Colour by secondary structure conservation
  37. New Feature JAL-4435
    Label sequence groups and tree internal nodes with diversity information
  38. Improvement JAL-4428
    integrate OSX codesigning scripts in jalview's repository
  39. New Feature JAL-4426
    Show number of sequences contributing to the consensus secondary structure in the status bar/tool tip
  40. Improvement JAL-4425
    optionally hide consensus/annotations when no data is available
  41. New Feature JAL-4424
    Add subtitle in PCA and Tree panel
  42. Improvement JAL-4420
    Jalview could recognise .features, .annotations and .newick files belonging to an alignment file when all dragged-and-dropped onto it
  43. Task JAL-4411
    Record source metadata in derived/transferred annotation rows
  44. New Feature JAL-4386
    Calculate tree using secondary structure annotation
  45. Bug JAL-4338
    PAE partition not shown in the same place when tree is closed and reopened, or layout changed, and cluster colours lost loading back from jalview project
  46. New Feature JAL-4233
    nf-core/proteinfold integration
  47. New Feature JAL-4219
    Parse RNA secondary structure annotation from 'extended' fasta-style files
  48. New Feature JAL-3987
    Consensus secondary structure annotation rows for sequences with multiple sources of structural data
  49. Bug JAL-3974
    HiDPI support in Windows
  50. Improvement JAL-3802
    View number of sequences per subgroup in a separate window
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