├── .travis.yml ├── CHANGELOG.md ├── LICENSE ├── MANIFEST.in ├── README.md ├── README_pypi.md ├── docs ├── scoary_manual.pdf └── tex │ ├── citations.bib │ ├── images │ ├── badlink.png │ ├── bestpossible.png │ ├── gene_presence_and_absence.png │ ├── goodlink.png │ ├── scoary_gui.png │ ├── scoary_logo.png │ └── worstpossible.png │ ├── scoary_manual.aux │ ├── scoary_manual.bbl │ ├── scoary_manual.blg │ ├── scoary_manual.dvi │ ├── scoary_manual.log │ ├── scoary_manual.pdf │ ├── scoary_manual.tex │ ├── scoary_manual.toc │ └── tables │ ├── t1.tex │ ├── t2.tex │ └── t3.tex ├── requirements.txt ├── scoary.py ├── scoary ├── GUI.py ├── __init__.py ├── citation.py ├── classes.py ├── exampledata │ ├── Example.vcf │ ├── ExampleTree.nwk │ ├── ExampleVCFTrait.csv │ ├── Gene_presence_absence.csv │ ├── Restrict_to.csv │ └── Tetracycline_resistance.csv ├── methods.py ├── nwkhandler.py └── vcf2scoary.py ├── setup.cfg ├── setup.py └── tests └── test_scoary_output.py /.travis.yml: 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