├── .github └── workflows │ └── build.yml ├── .gitignore ├── .travis.yml ├── LICENCE.txt ├── MANIFEST.in ├── README.rst ├── docs ├── Makefile ├── README.md ├── _static │ ├── css │ │ └── main.css │ └── images │ │ ├── example_ideal.png │ │ ├── pw_maze_dark.png │ │ ├── pw_maze_white.png │ │ └── title.png ├── conf.py ├── favicon.png ├── index.rst ├── logo_small.png ├── make.bat ├── makehtml.sh └── ref.rst ├── examples ├── data │ ├── phage_sequence.txt │ ├── sequence.gb │ ├── sequence_with_constraints.gb │ └── sequence_with_constraints.png ├── find_sequence_decomposition_with_mutations.py ├── generate_overhangs_set.py ├── ogabe_decomposition.py └── using_preferred_overhangs_sets.py ├── ez_setup.py ├── goldenhinges ├── OverhangSetOptimizer.py ├── OverhangsSelector.py ├── __init__.py ├── biotools.py ├── clique_methods.py ├── reports.py └── version.py ├── pypi-readme.rst ├── setup.py └── tests ├── test_basics.py ├── test_data ├── phage_sequence.txt └── sequence.gb └── test_reports.py 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