6.0.0
- Improvement in Miniprot post-processing for better performance (Issues #728, #739, #742, #744, #772, #795, #809)
- Update and incorporate plotting module - introduce --plot option (Issues #298, #638, #708, #731)
- Re-inroduce miniprot pipeline option for odb12 prokaryota datasets (Issue #816)
- Accept gzipped input files
- Update BBTools units (Issue #775)
- Allow odb10 and odb12 specific dataset downloads (Issue #784)
- Add job failure logs to busco.log file (Issue #755)
- Retain old log file in restart mode
- Decompress files in writeable location (Issues #693, #779, #789)
- Add inferred translation table to prokaryota batch summary (Issue #599)
- Fix compatibility with newer Python versions (Issue #805)

5.8.3
- Fix autolineage in offline mode (Issue #778)

5.8.2
- Add flexibility to SEPP placement to avoid crashes
- Remove manual check for mycoplasmatota

5.8.1
- Enhance compatibility with odb12 datasets; catch errors for unavailable pipelines

5.8.0
- Make code compatible with odb12 datasets
- Fix bug in full_table.tsv output (Issue #748)
- Fix quiet mode (Issue #756)
- Fix ZeroDivisionError edge case (Issue #760)

5.7.1
- Performance improvement in Miniprot post-processing (Issue #728)
- Restore *.fna files in Metaeuk pipeline (Issue #730)
- Bug fix (Issue #732)

5.7.0
- Make Miniprot pipeline the default option for eukaryote genomes
- Introduce optional --metaeuk flag to use Metaeuk pipeline for eukaryote genomes
- Add GFF files to miniprot pipeline
- Fix GFF files in metaeuk pipeline (Issue #624)
- Fix --skip_bbtools option in batch mode (Issue #721)

5.6.1
- Bug fixes
- Remove --update-data option and make it the default. To inactivate, use --offline

5.6.0
- Miniprot pipeline developed and retained as an option (--miniprot)
- Add miniprot prokaryota pipeline option
- Make -o (--out) parameter optional
- Introduce usage statistics reporting
- Datasets updated, including links to OrthoDB v10.1 (Issue #347)
- Fix symlink problems in Docker (Issue #602)
- Add option --skip_bbtools to skip BBtools run (Issue #641)
- Update HMMER post-processing

5.5.0
- Add miniprot pipeline (beta test)

5.4.7
- Fix bug in overlap handling (Issue #653): this fix also updated the way negative strand coordinates are reported,
i.e. <gene_id>:<start>-<stop> instead of <gene_id>:<low>-<high>
- Fix bug in HMMER result filtering (Issue #661)
- Fix bug in sequence trimming when exons are removed

5.4.6
- Fix mode setting bug in batch mode autolineage (Issue #636)
- Fix tab discrepancy bug in batch_summary.txt (Issue #643)
- Fix coordinate bug in overlap handling (Issue #644)

5.4.5
- Fix bug in overlap handling (Issues #627, #633)
- Fix bug in parasitic check (Issue #594)

5.4.4
- Fix bug in tar option (Issue #591)
- Fix edge case bug in overlap handling (Issue #592)
- Fix overlap adjustment algorithm and trim reported sequences
- Fix file open mode (Issue #622)
- Efficiency improvements with more parallel processing

5.4.3
- Fix bug in augustus --long pipeline (Issue #586)

5.4.2
- Fix batch summary statistics reporting bug in eukaryote pipeline

5.4.1
- Fix batch summary statistics reporting
- Fix compatibility with newer versions of BBMap
- Bug fixes

5.4.0
- Report complementary quality metrics using BBTools (Issue #552)
- Create GFF files and Nucleotide files for Metaeuk pipeline (Issues #268, #374, #449, #496)
- Reattempt connection to server in case of failure; also implemented a backup URL
- Fix quiet mode logging
- Bug fixes (including Issue #488, #509, #556, #575)

5.3.2
- Issue #544 fixed

5.3.1
- Issue #510 fixed
- Issue #542 fixed
- Bug fixes

5.3.0
- Introduce JSON summary file
- Issue #405 fixed
- Issue #491 fixed
- Issue #492 fixed
- Issue #493 fixed
- Issue #494 fixed
- Issue #497 fixed
- Issue #498 fixed
- Issue #517 fixed
- Issue #523 fixed

5.2.2
- Issue #390 fixed
- Issue #423 fixed
- Issue #464 fixed
- Issue #467 fixed
- Issue #470 fixed
- Add --tar option to compress some output folders

5.2.1
- Minor bug fixes

5.2.0
- Issue #224 fixed
- Issue #232 fixed
- Issue #266 fixed
- Issue #270 fixed
- Issue #352 fixed
- Issue #368 fixed
- Issue #386 fixed
- Introduce direct download option (Issues #252, #288)

5.1.3
- Issue #408 fixed
- Bug fixes

5.1.2
- Fix bug in batch  mode that affects Augustus runs

5.1.1
- Fix bug in batch mode

5.1.0
- Implement batch mode
- Issue #221 fixed
- Issue #328 fixed
- Issue #360 fixed
- Issue #388 fixed
- Issue #406 fixed
- Issue #415 fixed

5.0.0
- Implement metaeuk exon overlap filter
- Use metaeuk for eukaryote transcriptomes
- Issue #198 fixed
- Issue #248 fixed
- Issue #256 fixed
- Issue #260 fixed
- Issue #267 fixed
- Issue #277 fixed
- Issue #306 fixed
- Issue #313 fixed
- Issue #318 fixed
- Issue #326 fixed
- Issue #340 fixed
- Issue #344 fixed
- Issue #351 fixed
- Issue #357 fixed
- Issue #373 fixed
- Issue #385 fixed

5.beta.1
- Provide option to run augustus instead of metaeuk

5.beta
- Replace Augustus with Metaeuk

4.1.4
- Fix Augustus parsing bug

4.1.3
- Issue #296 fixed
- Issue #305 fixed
- Augustus parser improved

4.1.2
- Issue #295 fixed

4.1.1
- Issue #287 fixed

4.1.0
- Reintroduce restart mode (Issues #203, #229, #251)
- Fix augustus hanging problem (Issues #224, #232, #266)
- Allow multiple cores for BLAST 2.10.1+
- Issue #271 fixed
- Issue #247 fixed
- Issue #234 fixed

4.0.6
- Fix Augustus GFF parsing bug. Remove constraint on Augustus version.

4.0.5
- Constrain to use Augustus v3.2.3 on conda and Docker

4.0.4
- Fix inefficiency introduced in 4.0.3

4.0.3
- Issue #190 fixed
- Issue #191 fixed
- Issue #196 fixed
- Issue #200 fixed
- Reintroduce full retraining for all eukaryote runs

4.0.2
- Issue #182 partially fixed

4.0.1
- Issue #164 fixed
- Issue #166 fixed
- Issue #169 fixed
- Enforce single core on BLAST 2.4-2.10 to guarantee consistency of results. We recommend BLAST 2.2 or 2.3 for performance.

4.0.0
- Add the auto lineage selection through phylogenetic placement
- Introduce the automated downloads and updates of data files
- Use the OrthoDB v10 datasets, "_odb10", 166 lineages including archaea
- Add links to orthoDB in the file full_table.tsv
- Use Prodigal as gene predictor for non-eukaryotes
- Major refactoring of the code
- Main script is now called `busco`
- Improved logging system, notably to address issue #60 and to provide debug info without rerunning with debug=True
- Fix many minor bugs reported over years

3.1.0
- Add the additional script run_BUSCO_auto_lineage.sh

3.0.2
- The ~ character can be used in the config.ini file

3.0.1
- Add the environment variable BUSCO_CONFIG_FILE
- Add the –blast_single_core option
- Incompatibilities between plotting tool and config fixed

3.0.0
- Major refactoring of the code
- Introduce setup.py
- Introduce the config.ini file
- Issue #24 fixed
- Issue #25 fixed
- Switch to the MIT License

2.0.1
- Stop the execution when tblastn crashes, instead of just warning the user
- Issue #16 fixed
- Issue #9 fixed

2.0
- Minor changes, similar to beta 4

2.0 beta 4
- Sort the results by BUSCO ids in the full table output file
- Allow the user to pass custom Augustus parameters

2.0 beta 3
- Improve the detection of problematic special characters in the fasta header and sequences

2.0 beta
- The 1.0 code was debugged and new functionalities were added. See the user guide
