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JAL-4468
Add support for Ensemble Fasta format, used by Muscle5JAL-4458
parse PDB / mmCIF header/medata to improve autodetection of models, licensing and cross-references
drag and drop feature colours file to quickly apply feature settings
support plain TSV/csv/space separated import of PAEs and other list/matrix data
Allow specific format to be specified when importing a file via GUI and CLI
Support import of foldseek's m8 alignment files
Support Rfam 2020 style per sequence secondary structure lines in stockholm files
Parse RNA secondary structure annotation from 'extended' fasta-style filesJAL-4184
After exporting Fasta (.fa) to Stockholm (.sto) sequence descriptions are lost
Display trees embedded in multiple sequence alignment stockholm files
support for HSAML format or simialr
Read (and write) Relaxed PHYLIP formatted data
ncRNA and genes without product attributes are not imported from Genbank and EMBL format files
refactor stockholm parser so its quicker for PFAM full import
Sequence flatfile importer optionally strips out numbers/etcJAL-4028
Association with gff3 files seems unhelpful
Write alignments as phyloxml via Jalviews Fileformats system
FATCAT structure alignment import
Custom feature colours in BioJSON file are not preserved on import to Jalview
Import blastp results in SAM format
Parse LOCUS line of GenBank file to obtain possibly missing ACCESSION id (and other useful metadata)
Import and display alphafold predicted alignment error matrices from JSON
Support extended PDB ids
stockholm format does not guess database name correctly for sequence AC references
Jalview project files could contain bioschemas metadata about the contents of the file
Failing to reattach tree members to sequences IDs
Support 'mol_type' attribute for ENA/Genbank records
support import of gff2 alignments from exonerate coding2genome and cds2genome
specify colour of helix and sheet symbols via GUI and Annotation FileJAL-3722
Comprehensive testing of ENA and GenBank flatfile
Saving a file fails in Windows 10 in a particular (not known) circumstance
Loading a gzipped file and saving it leaves the new file uncompressed
Import phred quality scores
option to preserve sequence header (id) on save?
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
Combined row-wise and positional per-sequence annotation shading
include virtual feature tooltip in exported feature data
Provide option to include Jalview colourschemes in GFF output
Some file formats need to be submitted to EDAM ontology to allow their entry into bio.tools
Explore linkage with python library MODELLER
Preserve pfam and rfam metadata when exporting retrieved entries as Stockholm
whitespace at beginning of database accessions parsed from Stockholm files
UniProt accessions not written in Stockholm format from Pfam
Offer program specific IO options for GFF files
Offer option to filter features by length
provide support in Jalview for BSML files
Secondary structure annotation beyond DSSP-3 state interpreted as RNA extended base pair contacts in Stockholm files
Add support for 'pAS' 'sAS' and 'seq' Stockholm file annotation codes
StockholmFileTest not portable: does not cope with platform specific line endings
gffheader output with \n instead of System.getProperty("line.separator")
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