.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.4.
.TH DLESSP "1" "May 2016" "dlessP 1.4" "User Commands"
.SH NAME
dlessP \- Computes various p-values and other stats of interest for dless
.SH 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.
.SH OPTIONS
.HP
\fB\-\-msa\-format\fR, \fB\-i\fR FASTA|PHYLIP|MPM|MAF|SS
.IP
Alignment format (default is to guess format from file contents).
Note that the program msa_view can be used for conversion.
.HP
\fB\-\-refseq\fR, \fB\-M\fR <fname>
(for use with \fB\-\-msa\-format\fR 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.
.HP
\fB\-\-refidx\fR, \fB\-r\fR <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.
.HP
\fB\-\-timing\fR, \fB\-t\fR <file>
.IP
Write timing data to <file>.
.HP
\fB\-\-html\fR, \fB\-H\fR <dirname>
Create a directory and write one HTML file into it per DLESS
prediction, giving the stats for that prediction.
.HP
\fB\-\-help\fR, \fB\-h\fR
.IP
Show this help message and exit.