---
name: "dlessP"
section: "1"
platform: "linux"
package: "phast"
version: "1.7+dfsg-2"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/dlessP"
---

# dlessP(1)

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

## 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.