{
    "anvi_get_sequences_for_hmm_hits": {
        "--return-best-hit": true,
        "--align-with": "famsa",
        "--concatenate-genes": true,
        "--get-aa-sequences": true,
        "--hmm-sources": "Campbell_et_al",
        "--separator": "",
        "--min-num-bins-gene-occurs": "",
        "--max-num-genes-missing-from-bin": "",
        "--gene-names": "CoaE,FAD_syn,Flavokinase,Methyltransf_5,Peptidase_A8,Ribosomal_S20p",
        "threads": ""
    },
    "anvi_run_ncbi_cogs": {
        "run": false
    },
    "trimal": {
        "-gt": 0.5,
        "additional_params": "",
        "threads": ""
    },
    "iqtree": {
        "threads": 8,
        "-m": "WAG",
        "-bb": 1000,
        "additional_params": ""
    },
    "project_name": "TEST",
    "internal_genomes": "",
    "external_genomes": "external-genomes.txt",
    "fasta_txt": "fasta.txt",
    "output_dirs": {
        "PHYLO_DIR": "01_PHYLOGENOMICS",
        "LOGS_DIR": "00_LOGS"
    }
}
