NAME

       dlessP - Computes various p-values and other stats of interest for dless

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.