├── .eslintrc.js ├── .gitignore ├── .prettierrc ├── .travis.yml ├── LICENSE ├── README.md ├── benchmark ├── inserts │ ├── BoNT.fasta │ ├── gfp.fasta │ ├── human_HBB.fasta │ ├── insulin.fasta │ ├── luciferase.fasta │ └── oxytocin.fasta ├── requirements.txt ├── run.py └── targets │ ├── banth1.yaml │ ├── ecol.yaml │ ├── ngon.yaml │ └── paer.yaml ├── docs ├── Makefile ├── _static │ ├── logo5x.png │ └── verbose.gif ├── api.rst ├── cli.rst ├── conf.py ├── figures │ ├── make_figures.sh │ ├── no_original.html │ └── with_original.html ├── index.rst ├── methods.rst ├── requirements.txt └── usage.rst ├── examples ├── ecoli.heg.fna ├── ecoli.heg.yaml ├── freqgen.html ├── gfp.faa ├── gfp.fna ├── gfp_ecoli.fna └── recoded_gfp_2_mers.png ├── freqgen ├── __init__.py ├── __version__.py ├── cli.py ├── freqgen.py ├── generate.py ├── pyeasyga.py └── visualize.py ├── jest.config.js ├── lerna.json ├── logo ├── logo.sketch ├── logo.svg └── logo5x.png ├── package.json ├── packages ├── freqgen-cli │ ├── __tests__ │ │ └── addMaps_test.js │ ├── addMaps.js │ ├── cli.js │ ├── package-lock.json │ ├── package.json │ └── yaml.js ├── freqgen-core │ ├── __tests__ │ │ ├── distance_test.js │ │ ├── generate_test.js │ │ ├── kmerCounts_test.js │ │ ├── kmerFrequenciesFromSeq_test.js │ │ ├── kmerFrequencies_test.js │ │ ├── kmers_test.js │ │ ├── operators_test.js │ │ └── utilities_test.js │ ├── data │ │ ├── codons_for_aa.yaml │ │ ├── codons_without_synonyms.yaml │ │ ├── genetic_codes.yaml │ │ └── synonymous_codons.yaml │ ├── distance.js │ ├── generate.js │ ├── index.js │ ├── kmers.js │ ├── operators.js │ ├── package-lock.json │ ├── package.json │ └── utilities.js └── freqgen-ui │ ├── .browserslistrc │ ├── .eslintrc.js │ ├── .gitignore │ ├── README.md │ ├── babel.config.js │ ├── package-lock.json │ ├── package.json │ ├── postcss.config.js │ ├── public │ ├── favicon.ico │ └── index.html │ └── src │ ├── App.vue │ ├── assets │ └── logo.png │ ├── components │ ├── Main.vue │ ├── Navbar.vue │ ├── 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