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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-4466
    allow pairwise alignment gap parameters to be adjusted
  2. Improvement JAL-4461
    "Select format by extension" option in Jalview's "Save As" dialog's file type dropdown menu
  3. Epic JAL-4399
    Consensus annotations and Tree visualisations for sequence annotation
  4. Improvement JAL-4365
    Improve the Find window to indicate to/allow selection by users as to what is being searched
  5. Improvement JAL-4324
    Option to align after retrieval of sequences before display
  6. Improvement JAL-4309
    Redesign sequence ID tooltip to improve user experience
  7. New Feature JAL-4300
    New alignment windows from aligment webservices inherit feature settings and layout from input
  8. New Feature JAL-4299
    Copy format and layout settings from another alignment view
  9. Improvement JAL-4294
    Hidden Column arrows are pixel-out aligned with the vertical blue line, and almost hidden at left-hand side of alignment
  10. New Feature JAL-4292
    Fit to width alignment layout option
  11. Improvement JAL-4287
    Automatically discover and import alphaFold or best PDBe model when retrieving proteins from Uniprot
  12. New Feature JAL-4273
    Visible adjuster marks to grab and adjust annotation panel height and id width
  13. Improvement JAL-4231
    make it easier to pick preferred experimental modalities for structure data
  14. Improvement JAL-4213
    "add reference annotation" should ignore when a selection is active and not only add positions for currently highlighted columns/selection range
  15. Improvement JAL-4209
    Automatically add JNet result as reference sequence on the original alignment
  16. Improvement JAL-4204
    More precise control of sequence & alignment associated annotation row visibility
  17. Improvement JAL-4198
    add reference annotation should not by default only add annotation for selected columns
  18. New Feature JAL-4183
    Visualise hidden columns by introducing a gap in the alignment grid
  19. Bug JAL-4179
    Common nucleotide symbols turns sequence into 'protein', cannot set colour to 'nucleotide'
  20. Improvement JAL-4174
    Allow PAE file to be loaded for an already imported structure
  21. New Feature JAL-4138
    user preferences and structure chooser controls for automatically showing PAE annotation row along side pLDDT when loading structure from alphafold, and control secondary structure and temp factor display
  22. Improvement JAL-4112
    Suggestion for File Save dialog
  23. Improvement JAL-4094
    Shift-Click-Drag to adjust height of all annotation tracks of same type
  24. Improvement JAL-4093
    easier select-by-annotation and shade-by-annotation options
  25. Improvement JAL-4092
    Extend select/hide by annotation to offer highlight by as well
  26. Improvement JAL-4091
    Visual indication of relationship with associated sequence to distinguish different sequence associated annotation rows
  27. Epic JAL-4087
    Jalview GUI adapted for Touch and Gesture interactions
  28. New Feature JAL-4086
    Highlight aligned positions on all associated structures when mousing over a column
  29. Improvement JAL-4084
    Interactive highlights of sites on 3D structure corresponding for pAE matrix regions
  30. Improvement JAL-4069
    Sequence extent shows start-end for visible sequence range when residues at start or end are hidden
  31. New Feature JAL-4060
    nightingale style contact prediction track
  32. Story JAL-4055
    Should we retire the Jalview Desktop Window
  33. Bug JAL-4053
    The prev and next page buttons in the Sequence Fetcher FTS panel are often hidden
  34. Bug JAL-4051
    Disable Autosearch for index change in FTS Sequence Fetcher when autosearch is deselected
  35. Improvement JAL-4034
    Make the 3D-Beacons Search button more buttony and logic for Uniprot search
  36. New Feature JAL-3943
    Select/Fetch all button for database query results
  37. Improvement JAL-3926
    Autosearch disabled by default
  38. Story JAL-3925
    quick annotation of a structure via sequence features (that can be undone)
  39. Story JAL-3924
    total number of sequences in alignment not obvious when first loaded
  40. New Feature JAL-3772
    Prompt to save unsaved Alignment windows on close or quit
  41. Improvement JAL-3755
    Rendering multiple windows at once
  42. Improvement JAL-3728
    Java Console (and other independent JFrames) appear with default Java icon
  43. Improvement JAL-3710
    Find should report greedy matches only for conditional Regex
  44. Improvement JAL-3709
    Find dialog's 'Ignore hidden regions' setting isn't 'wysiwyg'
  45. Bug JAL-3699
    Loading a gzipped file and saving it leaves the new file uncompressed
  46. Improvement JAL-3693
    Preferences window can be opened more than once
  47. Epic JAL-3664
    UX for working with HMMs in Jalview
  48. New Feature JAL-3637
    Next/Previous region navigation buttons
  49. New Feature JAL-3623
    Combined row-wise and positional per-sequence annotation shading
  50. Epic JAL-3616
    Multiple Structure Viewer Support in Jalview 2.11.2
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