├── .gitignore ├── .travis.yml ├── COPYING.txt ├── Makefile ├── README.md ├── ci ├── conda_requirements.yml └── pip_requirements.txt ├── data ├── tm_align_output_10k.ali ├── tm_align_output_10k.tab └── zf-C2H2.hmm ├── deepblast ├── __init__.py ├── alignment.py ├── constants.py ├── dataset │ ├── __init__.py │ ├── alphabet.py │ ├── dataset.py │ ├── parse_blast.py │ ├── parse_fatcat.py │ ├── parse_hmmer.py │ ├── parse_mali.py │ ├── parse_pdb.py │ ├── parse_tm_align.py │ ├── tests │ │ ├── data │ │ │ ├── example.txt │ │ │ └── test_tm_align.tab │ │ ├── test_alphabet.py │ │ ├── test_dataset.py │ │ └── test_utils.py │ ├── tm_align.py │ └── utils.py ├── embedding.py ├── language_model.py ├── losses.py ├── metrics.py ├── nw.py ├── nw_cuda.py ├── ops.py ├── pretrained_models │ └── lstm2x.pt ├── score.py ├── sim.py ├── sw.py ├── sw_cuda.py ├── tests │ ├── cuda_timing.py │ ├── data │ │ ├── A.txt │ │ ├── ABC_tran.hmm │ │ ├── dm.txt │ │ ├── test.txt │ │ ├── theta.txt │ │ ├── train.txt │ │ ├── valid.txt │ │ └── zf-C2H2-alignments.txt │ ├── profile_nw.py │ ├── test_alignment.py │ ├── test_language_model.py │ ├── test_nw.py │ ├── test_nw_cuda.py │ ├── test_score.py │ ├── test_sw.py │ └── test_sw_cuda.py ├── trainer.py └── utils.py ├── examples └── simulation.py ├── imgs ├── example-alignment.png └── malidup.png ├── ipynb ├── small-test.ipynb ├── struct-benchmark.ipynb └── test_load_checkpoint.sh ├── scripts ├── deepblast-evaluate ├── deepblast-mali-align ├── deepblast-search ├── deepblast-tensorboard2csv ├── deepblast-train └── hmm-simulate └── setup.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/flatironinstitute/deepblast/HEAD/.gitignore -------------------------------------------------------------------------------- /.travis.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/flatironinstitute/deepblast/HEAD/.travis.yml 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