├── .gitignore ├── README.md ├── app ├── dense_retiever.py ├── retrieve_app-v2.py ├── retrieve_app-v3.py ├── retrieve_app-v4.py ├── retrieve_app-v5.py ├── retrieve_app-v6.py └── retrieve_app.py ├── data ├── __pycache__ │ └── data.cpython-38.pyc └── data.py ├── dense_encode ├── gen_t1000.py ├── gen_u90.py ├── generate_vec.py └── generate_vec_one.py ├── hmmer-batch ├── jack.sh ├── slurm-1920441.out ├── slurm-1920448.out ├── slurm-1920456.out ├── slurm-1922288.out ├── slurm-1942189.out ├── slurm-1942459.out ├── slurm-1942692.out └── submit.sh ├── model ├── __pycache__ │ └── model.cpython-38.pyc └── model.py ├── pics ├── .gitignore ├── pipeline.png └── train.png ├── requirements.txt ├── split ├── split_dataset_test.txt ├── split_dataset_train.txt ├── split_dataset_valid.txt ├── test.txt ├── train.txt └── valid.txt ├── test └── test.py ├── tools ├── count.py ├── do_sample.py ├── gen_test_seq_set.py ├── gen_top1000_msa.py ├── get_seq_from_name.py ├── get_size.py ├── hmm_aligner.py ├── meff_cal.py ├── myalign.py ├── score_sim.py ├── sel.py ├── split_ur90.py └── vis.py ├── train ├── main.py └── train.py └── utils ├── __pycache__ └── myutils.cpython-38.pyc └── myutils.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/heathcliff233/fastMSA/HEAD/.gitignore -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/heathcliff233/fastMSA/HEAD/README.md -------------------------------------------------------------------------------- /app/dense_retiever.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/heathcliff233/fastMSA/HEAD/app/dense_retiever.py -------------------------------------------------------------------------------- /app/retrieve_app-v2.py: 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