PROGRAM: dlessP

USAGE: dlessP [OPTIONS] alignment tree.mod predictions.gff > stats.tab

DESCRIPTION:

    Computes various p-values and other stats of interest for dless
    predictions and writes them to a tab-delimited file.  The 'alignment'
    and 'tree.mod' arguments should be as given to DLESS, and
    'predictions.gff' should be the output of DLESS.

OPTIONS:
    --msa-format, -i FASTA|PHYLIP|MPM|MAF|SS
        Alignment format (default is to guess format from file contents).  
	Note that the program msa_view can be used for conversion.

    --refseq, -M <fname>
        (for use with --msa-format MAF) Read the complete text of the
        reference sequence from <fname> (FASTA format) and combine it
        with the contents of the MAF file to produce a complete,
        ordered representation of the alignment.  The reference
        sequence of the MAF file is assumed to be the one that appears
        first in each block.

    --refidx, -r <refseq_idx>
        Use coordinate frame of specified sequence in output.  Default
        value is 1, first sequence in alignment; 0 indicates
        coordinate frame of entire multiple alignment.

    --timing, -t <file>
        Write timing data to <file>.

    --html, -H <dirname>
        Create a directory and write one HTML file into it per DLESS
        prediction, giving the stats for that prediction.

    --help, -h
        Show this help message and exit.