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

4.1.2
- 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
