├── .codecov.yml ├── .coveragerc ├── .flake8 ├── .gitattributes ├── .gitignore ├── .gitlab-ci.yml ├── AUTHORS.rst ├── CHANGELOG.rst ├── CONTRIBUTING.rst ├── GUNC_LOGO.svg ├── GUNC_favicon.svg ├── LICENSE ├── MANIFEST.in ├── README.rst ├── docs ├── Makefile ├── make.bat └── source │ ├── GUNC_LOGO.svg │ ├── _static │ ├── .placeholder │ └── GUNC_PLOT_example.png │ ├── authors.rst │ ├── changelog.rst │ ├── citations.rst │ ├── conf.py │ ├── contributing.rst │ ├── datasets.rst │ ├── functions.rst │ ├── index.rst │ ├── installation.rst │ ├── output.rst │ └── usage.rst ├── gunc ├── __init__.py ├── _version.py ├── checkm_merge.py ├── data │ ├── genome2taxonomy_gtdbref.tsv │ ├── genome2taxonomy_ref.tsv │ └── template.html ├── external_tools.py ├── get_scores.py ├── gunc.py ├── gunc_database.py ├── tests │ ├── __init__.py │ ├── test_data │ │ ├── test_genome.fa.diamond.out │ │ ├── test_genome.fa.diamond.out.chimerism_scores │ │ ├── test_genome.fa.genecalls.faa │ │ ├── test_genome.fa.gz │ │ ├── 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