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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. Bug JAL-4184
    After exporting Fasta (.fa) to Stockholm (.sto) sequence descriptions are lost
  2. New Feature JAL-4173
    Display trees embedded in multiple sequence alignment stockholm files
  3. New Feature JAL-4172
    support for HSAML format or simialr
  4. New Feature JAL-4162
    Read (and write) Relaxed PHYLIP formatted data
  5. Bug JAL-4100
    ncRNA and genes without product attributes are not imported from Genbank and EMBL format files
  6. Improvement JAL-4078
    refactor stockholm parser so its quicker for PFAM full import
  7. Improvement JAL-4029
    Sequence flatfile importer optionally strips out numbers/etc
  8. Story JAL-4028
    Association with gff3 files seems unhelpful
  9. New Feature JAL-4021
    Write alignments as phyloxml via Jalviews Fileformats system
  10. New Feature JAL-4003
    FATCAT structure alignment import
  11. Bug JAL-3936
    Custom feature colours in BioJSON file are not preserved on import to Jalview
  12. New Feature JAL-3894
    Import blastp results in SAM format
  13. Improvement JAL-3877
    Parse LOCUS line of GenBank file to obtain possibly missing ACCESSION id (and other useful metadata)
  14. New Feature JAL-3858
    Import and display alphafold alignment uncertainty matrices from JSON
  15. New Feature JAL-3856
    Support extended PDB ids
  16. Bug JAL-3846
    stockholm format does not guess database name correctly for sequence AC references
  17. New Feature JAL-3834
    Jalview project files could contain bioschemas metadata about the contents of the file
  18. Bug JAL-3831
    Failing to reattach tree members to sequences IDs
  19. Improvement JAL-3821
    Support 'mol_type' attribute for ENA/Genbank records
  20. Improvement JAL-3808
    support import of gff2 alignments from exonerate coding2genome and cds2genome
  21. Improvement JAL-3752
    specify colour of helix and sheet symbols via GUI and Annotation File
  22. Task JAL-3722
    Comprehensive testing of ENA and GenBank flatfile
  23. Bug JAL-3703
    Saving a file fails in Windows 10 in a particular (not known) circumstance
  24. Bug JAL-3699
    Loading a gzipped file and saving it leaves the new file uncompressed
  25. New Feature JAL-3641
    Import phred quality scores
  26. Improvement JAL-3630
    option to preserve sequence header (id) on save?
  27. Bug JAL-3628
    Unable to save update to an existing file on Windows due to 'something went wrong with the backups of this file' dialog when backups are disabled
  28. New Feature JAL-3623
    Combined row-wise and positional per-sequence annotation shading
  29. Improvement JAL-3569
    include virtual feature tooltip in exported feature data
  30. Improvement JAL-3568
    Provide option to include Jalview colourschemes in GFF output
  31. Task JAL-3545
    Some file formats need to be submitted to EDAM ontology to allow their entry into bio.tools
  32. Story JAL-3537
    Explore linkage with python library MODELLER
  33. Improvement JAL-3532
    Preserve pfam and rfam metadata when exporting retrieved entries as Stockholm
  34. Bug JAL-3531
    whitespace at beginning of database accessions parsed from Stockholm files
  35. Bug JAL-3529
    UniProt accessions not written in Stockholm format from Pfam
  36. Improvement JAL-3527
    Offer program specific IO options for GFF files
  37. New Feature JAL-3470
    Offer option to filter features by length
  38. New Feature JAL-3445
    provide support in Jalview for BSML files
  39. Bug JAL-3365
    Secondary structure annotation beyond DSSP-3 state interpreted as RNA extended base pair contacts in Stockholm files
  40. Improvement JAL-3307
    Add support for 'pAS' 'sAS' and 'seq' Stockholm file annotation codes
  41. Bug JAL-3259
    StockholmFileTest not portable: does not cope with platform specific line endings
  42. Bug JAL-3257
    gffheader output with \n instead of System.getProperty("line.separator")
  43. Bug JAL-3178
    Nonpositional features lose feature group on export as jalview features file
  44. Improvement JAL-3165
    Export T-Coffee scores and other alignment position score matrices
  45. Task JAL-3150
    Detect jalview version 1 project files and provide conversion instructions
  46. Improvement JAL-3123
    New statements in AnnotationFile to ensure single character column annotation can be exported/re-imported
  47. Bug JAL-3106
    Jalview uses '.jar' as default extension when saving projects
  48. New Feature JAL-3015
    Import new alignment data for existing sequences in dataset
  49. Improvement JAL-3012
    Avoid duplicating data when anonymising it for export to external analysis tool
  50. Improvement JAL-3004
    Optionally write sequence position in right-hand column of clustal files
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