USAGE
    HmmCleaner.pl <infiles> [options]

REQUIRED ARGUMENTS
    <infiles>
        list of alignment file to check with HmmCleaner

OPTIONS
    -costs <c1> <c2> <c3> <c4>
        Cost parameters that defines the low similarity segments detected by
        HmmCleaner. Default values are -0.15, -0.08, 0.15, 0.45 Users can
        change each value but they have to be in increasing order. c1 < c2 <
        0 < c3 < c4 Predefine value are also available with --large and
        --specificity options but user defined costs will be prioritary if
        present.

    --changeID
        Determine if output will have defline with generic suffix
        (_hmmcleaned)

    --noX
        Convert X characters to gaps that will not be taken into account by
        HmmCleaner.

    -profile=<profile>
        Determine how the profile will be create complete or leave-one-out
        (default: complete) leave-one-out = without the analyzed sequence
        (new profile each time) complete = all sequences (same profile for
        each sequence) First case is more sensitive but need more ressources
        (hence more time)

    --large
        Load predifined cost parameters optimized for MSA with at least 50
        sequences. Can be use with --specificity option. User defined costs
        will be prioritary if present.

    --specificity
        Load predifined cost parameters optimized to give more weigth on
        specificity. Can be use with --large option. User defined costs will
        be prioritary if present.

    --log_only
        Only outputs list of segments removed.

    --ali
        Outputs result file(s) in ali MUST format.

    -v[erbosity]=<level>
        Verbosity level for logging to STDERR [default: 0]. Available levels
        range from 0 to 5.

    --version
    --usage
    --help
    --man
        Print the usual program information
