├── LICENSE ├── README.md ├── README.pdf ├── VIBRANT_run.py ├── databases ├── VIBRANT_setup.py └── profile_names │ ├── VIBRANT_kegg_profiles.txt │ └── VIBRANT_vog_profiles.txt ├── example_data ├── Autolykiviridae_MG592481.1.fna ├── Microviridae_MH552510.2.faa ├── Podoviridae_KJ183192.1.fasta ├── example_PCA.pdf ├── example_output │ └── VIBRANT_mixed_example │ │ ├── VIBRANT_HMM_tables_parsed_mixed_example │ │ ├── mixed_example.KEGG_hmmtbl_parse.tsv │ │ ├── mixed_example.Pfam_hmmtbl_parse.tsv │ │ └── mixed_example.VOG_hmmtbl_parse.tsv │ │ ├── VIBRANT_HMM_tables_unformatted_mixed_example │ │ ├── mixed_example_unformatted_KEGG.hmmtbl │ │ ├── mixed_example_unformatted_Pfam.hmmtbl │ │ └── mixed_example_unformatted_VOG.hmmtbl │ │ ├── VIBRANT_figures_mixed_example │ │ ├── VIBRANT_figure_PCA_mixed_example.pdf │ │ ├── VIBRANT_figure_pathways_mixed_example.pdf │ │ ├── VIBRANT_figure_phages_mixed_example.pdf │ │ ├── VIBRANT_figure_quality_mixed_example.pdf │ │ └── VIBRANT_figure_sizes_mixed_example.pdf │ │ ├── VIBRANT_log_annotation_mixed_example.log │ │ ├── VIBRANT_log_run_mixed_example.log │ │ ├── VIBRANT_phages_mixed_example │ │ ├── mixed_example.phages_combined.faa │ │ ├── mixed_example.phages_combined.ffn │ │ ├── mixed_example.phages_combined.fna │ │ ├── mixed_example.phages_combined.gbk │ │ ├── mixed_example.phages_combined.txt │ │ ├── mixed_example.phages_lysogenic.faa │ │ ├── mixed_example.phages_lysogenic.ffn │ │ ├── mixed_example.phages_lysogenic.fna │ │ ├── mixed_example.phages_lytic.faa │ │ ├── mixed_example.phages_lytic.ffn │ │ └── mixed_example.phages_lytic.fna │ │ ├── VIBRANT_results_mixed_example │ │ ├── VIBRANT_AMG_counts_mixed_example.tsv │ │ ├── VIBRANT_AMG_individuals_mixed_example.tsv │ │ ├── VIBRANT_AMG_pathways_mixed_example.tsv │ │ ├── VIBRANT_annotations_mixed_example.tsv │ │ ├── VIBRANT_complete_circular_mixed_example.tsv │ │ ├── VIBRANT_figure_PCA_mixed_example.tsv │ │ ├── VIBRANT_genbank_table_mixed_example.tsv │ │ 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