├── .gitignore ├── DeepSequence ├── __init__.pyc ├── __pycache__ │ ├── helper.cpython-36.pyc │ ├── model.cpython-36.pyc │ └── train.cpython-36.pyc ├── helper.py ├── helper.pyc ├── model.py ├── model.pyc ├── train.py └── train.pyc ├── INSTALL ├── LICENSE ├── README.md └── examples ├── .ipynb_checkpoints ├── Downloading pretrained parameters-checkpoint.ipynb ├── Explore model outputs-checkpoint.ipynb └── Mutation Effect Prediction-checkpoint.ipynb ├── Explore model outputs.ipynb ├── Mutation Effect Prediction.ipynb ├── README.md ├── download_alignments.sh ├── download_pretrained.sh ├── logs └── .gitignore ├── mutations ├── BLAT_ECOLX_Ranganathan2015.csv ├── DLG4_RAT_Ranganathan2012.csv └── PABP_YEAST_Fields2013-singles.csv ├── params └── .gitignore ├── run_mle.py └── run_svi.py /.gitignore: -------------------------------------------------------------------------------- 1 | *.a2m 2 | *.fasta -------------------------------------------------------------------------------- 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