v0.3.0

• Adds improved documentation with tutorial
• Adds .summary.txt output file with summary statisics of Baktfold's performance (thanks @mbhall88 for the suggestion)
• e.g.

Annotation:
CDS count: 2635
CDS beginning hypotheticals: 55
CDS annotated with Baktfold database hit: 12
CDS annotated with Baktfold function: 7
CDS remaining hypotheticals: 48

Baktfold:
Software: v0.2.0
Database: v0.1.0
DOI: https://doi.org/10.64898/2026.03.31.715528
URL: github.com/gbouras13/baktfold

v0.2.0

• Add support for bakta_proteins JSON output format as baktfold proteins input - baktfold proteins will automatically detect the format (.faa or Bakta JSON) #30
• Fix tool description in JSON (inherits Bakta's and add Baktfold's) #27
• Adds comprehensive CI tests synced to Setonix via @ignatiusm HPCI, getting around GitHub CI runner difficulties (and adding GPU access)

v0.1.1

• Support Uniprot/Trembl etc protein headers with baktfold proteins that Foldseek trims by default
• Fix bug where embeddings were cast to half precision with --cpu #28

v0.1.0

• Changes to Baktfold database hosting - now on HuggingFace so should be much much faster by default to download
• Introduction of baktfold convert-prokka for automatically converting a Prokka GenBank to the required Bakta JSON format
• If you have a prokaryotic genome annotated with other methods, we recommend genbank_to for non-Bakta GenBank conversion to Bakta JSON format
• Experimental support for eukaryotes
  • Via baktfold convert-euk for automatically converting a eukaryotic GenBank to the required Bakta JSON format
  • Then pass the --euk flag with baktfold run
• All eukaryote CDS features should be annotated - the glue-code and standards compliance support for other genomic features is not guaranteed.
  • Please try it out and reach out if you have any feedback

v0.0.3

Baktfold is currently under active development. We would welcome any and all feedback (especially bugs) via Issues

• Keeps all non-overlapping top hits for CATH, not just the tophit (as multi-domain proteins can and should have multiple different hits to CATH). This is equivalent to using --greedy-best-hits with Foldseek

v0.0.2 - beta release 2

Baktfold is currently under active development. We would welcome any and all feedback (especially bugs) via Issues

• Fixes #3 allowing for bioconda integration

v0.0.1 - beta release

Baktfold is currently under active development. We would welcome any and all feedback (especially bugs) via Issues

• Initial beta release v.0.0.1 (will by on Pypi/Conda)