ProtHint v2.6.0

Major changes

• Fixed translation of incomplete seed genes

Other changes

• Several bug fixes, mostly for the iterative mode
• Removed all ProSplign-related code

ProtHint v2.5.0

Major changes

• Improved speed by running Spaln in batches
  • This can lead to up to 90% speed improvement, depending on the genome
• A single output file which is directly compatible with BRAKER and AUGUSTUS is now produced
• ProSplign is no longer supported

Other changes

• Added a time left estimate
• Added a fungal mode
• Various edge case error fixes

ProtHint v2.4.0

Major changes

• Implemented an iterative mode
  • Next iteration of ProtHint is only executed for gene seeds which differ
    from previous iteration's gene seeds. Gene IDs of hints which correspond
    to identical gene seeds are updated to match the IDs of the new seed genes.

Other changes

• Bug fix: Print CDSpart in top_chains.gff

ProtHint v2.3.0

Major changes

• Updated the default maximum number of target proteins which are spliced
  aligned per seed gene
  • Changed from 250 to 25 based on the observation that using more than 25
    protein targets does not lead to a significant increase in sensitivity
    of hints
  • The change leads to ~10x faster runtime
• The default filtering thresholds for High-Confidence hints were updated to
  accommodate for the change in the maximum number of target proteins
• Transition from Python 2 to Python 3

Other changes

• Refactored code for system and dependency calls
  • Check whether system/dependency call finished successfully
  • If a dependency is not found in the dependency folder, ProtHint looks
    for the dependency in the PATH
• Added output with chained hints corresponding to the best aligned protein
  per gene seeds -- this output is used by Augustus
  in BRAKER

ProtHint v2.2.0

Major changes

• Bug fix: Frameshifts are no longer reported as introns in the output

Other changes

• Reorganized project structure: Spaln and ProSplign alignment scorers were
  moved to separate repositories
• Improved installation and run instructions

ProtHint v2.1.1

• Added the option to run final alignment with ProSplign
  • Spaln is still used to pre-select proteins for alignment, as a speed-up

ProtHint v2.1.0

• Improved filtering of high confidence starts

ProtHint v2.0.0

Major changes

• Output is now directly parsed and filtered from Spaln, ProSplign step is omitted
  • This change significantly improves the runtime (3x-20x speedup depending on
    the genome size)
• Improved sensitivity of all reported hints (in prothint.gff file) due to changes
  in the filtering procedure, especially for very remote proteins

Other changes

• Added usage example
• Added printing of progress messages
• Added a cleanup option

ProtHint v1.0.0

• Initial release which uses ProSplign for final spliced alignment and Spaln only as a speed-up step