├── .gitattributes ├── .github └── workflows │ └── check_version.yaml ├── .gitignore ├── .pre-commit-config.yaml ├── CITATION.bib ├── LICENSE ├── README.md ├── assets ├── diagram.txt ├── domain_plot.png ├── phylogenetic.png ├── predictions.png ├── resistify.ipynb └── terminal.png ├── pixi.lock ├── pyproject.toml ├── resistify ├── __init__.py ├── __version__.py ├── _loguru.py ├── annotations.py ├── bin │ └── biocrf-static ├── coconat.py ├── data │ ├── MLP_CC_extEDVID.pkl │ ├── MLP_LRR_LxxLxL.pkl │ ├── MLP_NBS_GLPL.pkl │ ├── MLP_NBS_MHD.pkl │ ├── MLP_NBS_P-loop.pkl │ ├── MLP_NBS_RNSB-A.pkl │ ├── MLP_NBS_RNSB-B.pkl │ ├── MLP_NBS_RNSB-C.pkl │ ├── MLP_NBS_RNSB-D.pkl │ ├── MLP_NBS_VG.pkl │ ├── MLP_NBS_Walker-B.pkl │ ├── MLP_TIR_aA.pkl │ ├── MLP_TIR_aC.pkl │ ├── MLP_TIR_aD3.pkl │ ├── MLP_TIR_bA.pkl │ ├── MLP_TIR_bC.pkl │ ├── MLP_TIR_bD-aD1.pkl │ ├── crfModel │ ├── dlModel.ckpt │ ├── nlrdb.hmm │ ├── nlrexpress.fasta │ ├── prrdb.hmm │ └── tmbed_models │ │ ├── cv_0.pt │ │ ├── cv_1.pt │ │ ├── cv_2.pt │ │ ├── cv_3.pt │ │ └── cv_4.pt ├── download_models.py ├── draw.py ├── hmmsearch.py ├── main.py ├── nlrexpress.py ├── tmbed.py └── utility.py └── tests ├── data ├── fls2.fa ├── nlr_coconat_expected │ ├── annotations.tsv │ ├── coconat.tsv │ ├── domains.tsv │ ├── motifs.tsv │ ├── nbarc.fasta │ ├── nlr.fasta │ └── results.tsv ├── nlr_expected │ ├── annotations.tsv │ ├── domains.tsv │ ├── motifs.tsv │ ├── nbarc.fasta │ ├── nlr.fasta │ └── results.tsv ├── nlr_retain_coconat_expected │ ├── annotations.tsv │ ├── coconat.tsv │ ├── domains.tsv │ ├── motifs.tsv │ ├── nbarc.fasta │ ├── nlr.fasta │ └── results.tsv ├── nlr_retain_expected │ ├── annotations.tsv │ ├── domains.tsv │ ├── motifs.tsv │ ├── nbarc.fasta │ ├── nlr.fasta │ └── results.tsv ├── prr_expected │ ├── annotations.tsv │ ├── domains.tsv │ ├── motifs.tsv │ ├── prr.fasta │ └── results.tsv └── zar1.fa └── test_resistify.py /.gitattributes: -------------------------------------------------------------------------------- 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