{
    "BASIC": {
        "RUN_NAME": "20220622-152845",
        "MODE": "identification",
        "QUERY_ONLY": true,
        "EMAIL": "wan101010@snu.ac.kr",
        "GENE": [
           "ITS" , "BenA", "RPB2", "CaM"     ],
        "CONCATENATE": true,
        "DB": [
            "DB_Penicillium.xlsx"
        ],
        "MAXIMUM_OUTGROUP_COUNT": 3
    },
    "METHOD": {
        "NEW_RUN": true,
        "RUNNING_FROM": "visualize",
        "SEARCH_METHOD": "mmseqs",
        "ALIGNMENT_METHOD": "mafft",
        "TRIMMING_METHOD": "none",
        "MODEL_METHOD": "none",
        "TREE_METHOD": "fasttree"
    },
    "VISUALIZE": {
        "BOOTSTRAP_CUTOFF": 70,
        "DESIGNATED_GENUS": "unknowngenus",
        "SHORTEN_GENUS": true,
        "CONST_WIDTH": 1000,
        "CONST_HEIGHT": 6,
        "CONST_MAX_LENGTH": 48,
        "BLACK": "#000000",
        "HIGHLIGHT": "#bb0000",
        "SOURCECOLOR": [
            "#14c4e4",
            "#c4e414",
            "#e49c14",
            "#145ce4"
        ],
        "BGCOLOR": [
            "#f4f4f4",
            "#c6c6c6"
        ],
        "OUTGROUPCOLOR": "#999999",
        "FONT_TYPE": "Arial",
        "FONT_SIZE": 10,
        "FONT_SIZE_BOOTSTRAP": 9
    },
    "OPTIONAL": {
        "THREADS": 12,
        "REGEX_QUERY": [
        ],
        "CLUSTERING_CUTOFF": 0.97,
        "INCLUDE_AMBIGUOUS_SEQS" : true,
        "MAFFT_ALGORITHM": "auto",
        "TRIMAL_ALGORITHM": "gt",
        "COLLAPSING_CUTOFF": 0.01,
        "BOOTSTRAP": 1000,
        "SOLVE_FLAT": true,
        "ZERO": 1.00000050002909e-06
    },
    "ADVANCED": {
        "DEBUG": true,
        "CONFIDENT_DB": true,
        "SPECIES_BLACKLIST": [
            "sp."
        ],
        "USE_DEFAULT_GENUS_LIST" : true,
        "SAVE_SEARCH_MATRIX": true,
        "SAVE_SEARCH_RESULT": true,
        "MATRIX_FORMAT" : "csv",
        "HIERACHY_OUTGROUP": "section",
        "WORD_SIZE": 7,
        "E-VALUE": 0.00000001,
        "MAX_ITERATE": 1000,
        "gt": 0.2,
        "op": 1.3,
        "ep": 0.1,
        "AVX": true,
        "SAVE_RUN": true,
        "SAVE_SEARCH_DB" : true,
        "USE_SAVED_DB" : true
    }
}