├── .github ├── dependabot.yml └── workflows │ ├── python-publish.yml │ └── run_example.yml ├── .gitignore ├── COPYING ├── COPYING.LESSER ├── LICENSE ├── README.md ├── example_data ├── UP000005640_9606.fasta ├── UP000005640_9606.omamer └── UP000005640_9606.sum ├── pyproject.toml ├── src └── omark │ ├── __init__.py │ ├── assets │ ├── summarized_report.txt │ └── textual_report.txt │ ├── cli.py │ ├── files.py │ ├── graphics.py │ ├── omamer_species_placement.py │ ├── omamer_utils.py │ ├── omark.py │ ├── scoring.py │ ├── species_determination.py │ └── utils.py └── utils ├── Contamination_chromosome_filtering.ipynb ├── Contextualize_OMA.ipynb ├── Explore_Data.ipynb ├── contamination_chromosome_filtering.py ├── genome_simulation.py ├── mapping_template.txt ├── omark_contextualize.py └── plot_all_results.py /.github/dependabot.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DessimozLab/OMArk/HEAD/.github/dependabot.yml 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