Provided by: phast_1.4+dfsg-1_amd64 
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.