├── .gitignore ├── README.md ├── data ├── chimp_data.txt ├── dengue.fasta ├── dog_data.txt ├── flavobacteriaceae.fasta ├── human_data.txt ├── human_data_compressed ├── human_data_uncompressed.txt ├── sample.fa └── sample.fq ├── dmc-compress-test.ipynb ├── dna-notes.ipynb ├── dna-sample-analysis.ipynb ├── dynamic-markov-compression.ipynb ├── images ├── arithmetic-coding.png ├── cloning.png ├── first-order-chain.png ├── frequency-calculation.png ├── k=1-markov-dengue.png ├── k=2-markov-dengue.png ├── probability-table.png └── second-order-chain.png ├── library ├── HOMarkov │ ├── __init__.py │ └── markov.py ├── dmc └── dmc.c ├── markov-arithmetic-implementation.ipynb └── requirements ├── conda-requirements.txt └── requirements.txt /.gitignore: -------------------------------------------------------------------------------- 1 | 2 | .DS_Store 3 | -------------------------------------------------------------------------------- /README.md: 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