What's new? (History)

Version 1.6.0

Released 24 November 2025

  • Switch to ONNX for model storage. This makes the models more portable between versions
  • Fix float counts in Paladin mapping (#74)
  • Fix some issues in MacOS

Version 1.5.0

Released 20 September 2024

  • Add support for local searching when querying the AMPSphere database
  • Slightly change output format for AMPSphere matching
  • Add --verbose and --quiet flags

Version 1.4.0

Released 27 June 2024

Version 1.3.0

Released 5 December 2023

  • Adds density estimates to output
  • Adds compatibility with Pyrodigal ≥3

Version 1.2.0

Released May 9 2022

  • Adopt pyrodigal v.0.7.3 to predict genes
  • Implement a hybrid gene prediction system: training mode for contigs > 100kbp and use pre-trained models for smaller contigs

Bugfixes

  • Fix the README files generation by the output type

Version 1.1.0

Released November 8 2021

  • Add support for bzip2 and xz compressed FASTA files
  • Eliminate R dependency
  • Include more extensive testing
  • New feature computation code (Python implementation) made macrel about 3.5 times faster than before:
Time \ Code version 1.0.1 version 1.1.0
Real 60m 44.380s 17m 15.313s
User 33m 37.604s 9m 38.034s
System 0m 16.076s 0m 6.270s

Bugfixes

  • Fix abundance/reads modes when single-ended reads were used

Version 1.0.1

Released September 2 2021

Bugfixes

  • No longer crash on very short peptides (1 or 2 amino acids)

Version 1.0.0

Released December 21 2020

User-visible improvements

  • Add README.md files to the output directories documenting the output files

Version 0.6.1

Released October 29 2020

User-visible improvements

  • Atomicwrites is now an optional dependency. This implies a loss of functionality if not available (file writing is no longer atomic), but the atomicwrites dependency caused issues (especially on Mac)

Version 0.6.0

Released October 10 2020

User-visible improvements

  • Add --log-file and --log-append command line arguments
  • Add usage example in command line help message
  • Output is now written atomically (i.e., no partial files)

Version 0.5.0

Released May 11 2020

User visible changes

  • Fix bug with Prodigal by changing internal parameters. Although this is a bugfix, it will also change the results in some cases.
  • Output table now includes the version on the header

Bugfixes

  • Fix bug with using --force and existing directories

Version 0.4.0

Released March 16 2020

User-visible improvements

  • Add --keep-negatives flag

  • Add warning for longer sequences

  • Remove Methionine from N-terminus

Bugfixes

  • Fix for when no smORFs are present

Version 0.3.1

Released January 24th 2020

Bugfixes

  • Fix for Python 2.7

Version 0.3.0

Released January 24th 2020

User-visible improvements

  • Add get-examples command
  • Add get-smorfs command

Internal improvements

  • Convert to scikit-learn
  • Updated training sets
  • Fix license (must be GPL because of Peptides)

Version 0.2.0

Released January 14th 2020

  • Complete release