├── .gitignore ├── .travis.yml ├── LICENSE.txt ├── MANIFEST.in ├── README.md ├── bacphlip ├── __init__.py ├── bacphlip.py ├── command_line.py └── data │ ├── example_data │ ├── genome_example.fasta │ ├── genome_example.fasta.6frame │ ├── genome_example.fasta.bacphlip │ ├── genome_example.fasta.hmmsearch │ ├── genome_example.fasta.hmmsearch.tsv │ ├── genome_example_2.fasta │ ├── genome_example_2.fasta.6frame │ ├── genome_example_2.fasta.bacphlip │ ├── genome_example_2.fasta.hmmsearch │ ├── genome_example_2.fasta.hmmsearch.tsv │ ├── multi_example.fasta │ ├── multi_example.fasta.BACPHLIP_DIR │ │ ├── NC_001416.1.6frame │ │ ├── NC_001416.1.hmmsearch │ │ ├── NC_001416.1.hmmsearch.tsv │ │ ├── NC_001604.1.6frame │ │ ├── NC_001604.1.hmmsearch │ │ └── NC_001604.1.hmmsearch.tsv │ ├── multi_example.fasta.bacphlip │ └── multi_example.fasta.hmmsearch.tsv │ ├── prot_models.hmm │ └── rf_best.joblib ├── codecov.yml ├── paper ├── BACPHLIP_supplement.pdf ├── paper.bib └── paper.md ├── pytest.ini ├── 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