├── .github └── workflows │ └── action.yml ├── .gitignore ├── .readthedocs.yml ├── .test ├── annotations │ └── TIGRFAMs_annotation.ann ├── config.yaml ├── config_learnapp.yaml ├── input │ ├── NapB.faa │ ├── NapD.faa │ └── nirS.faa ├── input_learnapp │ ├── UP000322080_2603819.fasta │ └── UP000322981_424902.fasta └── test-env.yml ├── LICENSE ├── README.md ├── docs ├── Makefile ├── make.bat └── source │ ├── background │ ├── ml.rst │ ├── overview.rst │ └── params.rst │ ├── conf.py │ ├── getting_started │ ├── cli.rst │ ├── config.rst │ ├── install.rst │ └── usage.rst │ ├── index.rst │ ├── refs.bib │ ├── requirements.txt │ ├── troubleshooting │ └── common.rst │ └── tutorial │ ├── index.rst │ ├── snekmer_demo.ipynb │ ├── snekmer_learnapp_tutorial.ipynb │ └── snekmer_motif_tutorial.ipynb ├── environment.yml ├── environment_BSF.yml ├── environment_Windows.yml ├── requirements.txt ├── resources ├── LA_config.yaml ├── README.md ├── annotations │ └── TIGRFAMs_annotation.ann ├── clust.yaml ├── config.yaml ├── data │ └── NCBI_RepRef_N-cycling_families_v2.0.tgz ├── favicon.svg ├── kmer-association-example │ ├── InterPro_annotation.txt.gz │ ├── annotations │ │ └── InterPro.ann │ ├── config.yaml │ ├── input │ │ └── UP000031546_45670.fasta │ └── ten_genomes │ │ ├── UP000004358_314230.fasta.gz │ │ ├── UP000031546_45670.fasta.gz │ │ ├── UP000056630_1739114.fasta.gz │ │ ├── UP000057938_361183.fasta.gz │ │ ├── UP000198893_569882.fasta.gz │ │ ├── UP000199134_645273.fasta.gz │ │ ├── UP000199168_556533.fasta.gz │ │ ├── UP000239203_155976.fasta.gz │ │ ├── UP000305778_2571141.fasta.gz │ │ └── UP000323646_2593411.fasta.gz ├── motif_config.yaml ├── snekmer_logo.png ├── snekmer_workflow.svg └── tutorial │ ├── demo_example │ ├── input │ │ ├── TIGR03149.faa │ │ └── nxrA.faa │ └── run_demo.sh │ ├── learnapp_tutorial_files │ ├── inputs │ │ ├── UP000317332_2567861.fasta │ │ ├── UP000317977_2528013.fasta │ │ ├── UP000319088_2600309.fasta │ │ ├── UP000319374_2585119.fasta │ │ ├── UP000319639_2592816.fasta │ │ ├── UP000319776_92403.fasta │ │ ├── UP000319825_1880.fasta │ │ ├── UP000319897_1715348.fasta │ │ ├── UP000480288_2708300.fasta │ │ ├── UP000480297_2681465.fasta │ │ ├── UP000481030_1602942.fasta │ │ └── UP000482960_1076125.fasta │ └── run_LA_demo.sh │ ├── motif_tutorial_files │ ├── input │ │ ├── TIGR03149.faa │ │ └── nxrA.faa │ └── run_demo.sh │ ├── snekmer_demo.ipynb │ ├── snekmer_learnapp_tutorial.ipynb │ └── snekmer_motif_tutorial.ipynb ├── setup.py └── snekmer ├── __init__.py ├── _version.py ├── alphabet.py ├── cli.py ├── cluster.py ├── io.py ├── model.py ├── motif.py ├── plot.py ├── report.py ├── rules ├── apply.smk ├── cluster.smk ├── evaluate.smk ├── kmerize.smk ├── learn.smk ├── model.smk ├── motif.smk ├── process.smk └── search.smk ├── score.py ├── scripts ├── cluster_cluster.py ├── model_model.py ├── model_score.py ├── motif_motif.py ├── motif_preselect.py └── motif_rescore.py ├── templates ├── cluster_template.html ├── model_template.html ├── 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