├── .github └── workflows │ └── linux.yml ├── Dockerfile ├── LICENSE.TXT ├── README.TXT ├── README.md ├── cpanfile ├── docs ├── experiment_results │ └── simone.report.txt ├── figs │ ├── alex-katharina-tomas.png │ ├── best_by_compleasm.jpg │ ├── braker-es.odg │ ├── braker-es.pdf │ ├── braker-es.png │ ├── braker-intercept.odg │ ├── braker-intercept.png │ ├── braker1.pdf │ ├── braker1.png │ ├── braker2-full.pdf │ ├── braker2-full.png │ ├── braker2.pdf │ ├── braker2.png │ ├── braker2_ep.odg │ ├── braker2_ep.pdf │ ├── braker2_ep.png │ ├── braker2_ep_prothint.odg │ ├── braker2_ep_prothint.png │ ├── braker3_etp.png │ ├── lars.jpg │ ├── mario.png │ └── mark.png ├── long_reads │ └── long_read_protocol.md ├── posters │ ├── poster_PAG2015.pdf │ ├── poster_PAG2018.pdf │ ├── poster_PAG2019.pdf │ ├── poster_PAG2020.pdf │ ├── poster_PAG2023.pdf │ └── poster_PAG2024.pdf └── slides │ ├── slides_PAG2015.pdf │ ├── slides_PAG2018.pdf │ ├── slides_PAG2020.pdf │ ├── slides_PAG2022.pdf │ ├── slides_PAG2023.pdf │ └── slides_PAG2024.pdf ├── example ├── README.md ├── RNAseq.hints ├── docker-tests │ ├── test1.sh │ ├── test2.sh │ └── test3.sh ├── genome.fa ├── proteins.fa ├── results │ ├── test1 │ │ ├── augustus.hints.aa │ │ ├── augustus.hints.gtf │ │ ├── braker.gtf │ │ ├── genemark.gtf │ │ └── hintsfile.gff │ ├── test2 │ │ ├── augustus.hints.aa │ │ ├── augustus.hints.gtf │ │ ├── braker.gtf │ │ ├── genemark.gtf │ │ └── hintsfile.gff │ ├── test3 │ │ ├── augustus.hints.aa │ │ ├── augustus.hints.gtf │ │ ├── braker.gtf │ │ ├── genemark.gtf │ │ └── hintsfile.gff │ ├── test3_4 │ │ ├── augustus.hints.aa │ │ ├── augustus.hints.gtf │ │ ├── braker.gtf │ │ ├── genemark.gtf │ │ └── hintsfile.gff │ ├── test4 │ │ ├── augustus.hints.aa │ │ ├── augustus.hints.gtf │ │ ├── braker.gtf │ │ └── hintsfile.gff │ ├── test5 │ │ ├── augustus.ab_initio.aa │ │ ├── augustus.ab_initio.codingseq │ │ ├── augustus.ab_initio.gtf │ │ ├── braker.gtf │ │ └── genemark.gtf │ ├── test6 │ │ ├── augustus.hints.aa │ │ ├── augustus.hints.codingseq │ │ ├── augustus.hints.gtf │ │ ├── bam_header.map │ │ ├── braker.gtf │ │ ├── genemark.gtf │ │ ├── genome_header.map │ │ ├── gthTrainGenes.gtf │ │ └── hintsfile.gff │ └── test7 │ │ ├── augustus.hints.aa │ │ ├── augustus.hints.codingseq │ │ ├── augustus.hints.gtf │ │ ├── bam_header.map │ │ ├── genome_header.map │ │ └── hintsfile.gff ├── singularity-tests │ ├── test1.sh │ ├── test2.sh │ └── test3.sh ├── subsampled_viri.fa └── tests │ ├── test1.sh │ ├── test1_restart1.sh │ ├── test1_restart2.sh │ ├── test1_restart3.sh │ ├── test2.sh │ ├── test2_restart1.sh │ ├── test2_restart2.sh │ ├── test2_restart3.sh │ ├── test3.sh │ ├── test3_4.sh │ ├── test3_restart1.sh │ ├── test3_restart2.sh │ ├── test3_restart3.sh │ ├── test4.sh │ ├── test5.sh │ ├── test5_restart2.sh │ ├── test5_restart3.sh │ ├── test6.sh │ └── test7.sh ├── scripts ├── README.braker ├── braker.pl ├── braker_cleanup.pl ├── cfg │ ├── ep.cfg │ ├── ep_utr.cfg │ ├── etp.cfg │ ├── gth.cfg │ ├── gth_utr.cfg │ ├── rnaseq.cfg │ └── rnaseq_utr.cfg ├── compare_intervals_exact.pl ├── compute_accuracies.sh ├── dev │ ├── analyse_prothint.pl │ ├── log_reg.R │ ├── maker_utrs_to_augustus.pl │ └── rename_busco_genes.py ├── downsample_traingenes.pl ├── ensure_n_training_genes.py ├── filterGenemark.pl ├── filterIntronsFindStrand.pl ├── filter_augustus_gff.pl ├── findGenesInIntrons.pl ├── gatech_pmp2hints.pl ├── get_etp_hints.py ├── get_gc_content.py ├── helpMod_braker.pm ├── licence.txt ├── license.txt ├── list_of_changes ├── log_reg_prothints.pl ├── sortGeneMark.py └── stringtie2utr.py └── t ├── 01.helper.t ├── 02.clean-abort.t ├── data └── sequence.gb └── lib └── Test └── BRAKER.pm /.github/workflows/linux.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Gaius-Augustus/BRAKER/HEAD/.github/workflows/linux.yml -------------------------------------------------------------------------------- /Dockerfile: 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