Complete list of Parameters

###TO SORT OUT

    -h, --help
          Display the help message.
    -k, --klen INTEGER
          Kmer Length. Default: 3.
    -d, --debug
          Debug Messages.
    -q, --query-file INPUT_FILE
          Path to the file containing your query sequence data.
    -r, --reference-file INPUT_FILE
          Path to the file containing your reference sequence data.
    -p, --pairwise-file INPUT_FILE
          Path to the file containing your sequence data which you will perform pairwise comparison on.
    -m, --markov-order INTEGER
          Markov Order Default: 0.
    -o, --output-file OUTPUT_FILE
          Output file.
    -n, --num-hits INTEGER
          Number of top hits to return when running a Ref/Query search. If you want all the result, enter 0. Default:
          10.
    -t, --distance-type STRING
          The method of calculating the distance between two sequences. For descriptions of distance please refer to
          the wiki. One of d2, euclid, d2s, d2star, manhattan, chebyshev, dai, bc, ngd, and all. Default: d2.
    -s, --sequence-type STRING
          Define the type of sequence data to work with. One of dna, aa, and raa. Default: dna.
    -f, --output-format STRING
          For Reference/query based usage you can select your output type. One of default, tabular, and blastlike.
          Default: default.
    -nr, --no-reverse
          Do not use reverse compliment.
    -gc, --calc-gc
          Calculate GC content of query/ref in search mode.
    -nh, --no-header
          Do not print header when performing search mode.
    -mask, --skip-mer List of STRING's
          Specify binary masks where a zero indicates skipping that base and one keeps it. e.g. 01110.
    -c, --num-cores INTEGER
          Number of Cores. Default: 1.
    --version
          Display version information.