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.

dlessP 1.4                                          May 2016                                           DLESSP(1)