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

# consEntropy(1)

For use with phastCons. Given phylogenetic models for conserved and

## NAME

consEntropy - For use with phastCons.  Given phylogenetic models for conserved and

## DESCRIPTION

For use with phastCons. Given phylogenetic models for conserved and

-

  non-conserved states, the target coverage, and the (prior) expected length of a conserved element, compute the relative entropy (H) of the phylogenetic models, the expected minimum number of conserved sites required to predict conserved element (L\_min), the "phylogenetic information threshold" (PIT = L\_min \* H), and the expected maximum number of nonconserved sites tolerated within a conserved element (L\_max).  Also will make a recommendation for a new prior expected length based on a given target value of L\_min\*H (see **--LminH**).

## SYNOPSIS

consEntropy \[OPTIONS\] \<target-coverage\> \<expected-length\> \\

-

  \[ \<cons.mod\> \<noncons.mod\> \]

## OPTIONS

**--H**, **-H** \<value\>

-

  Instead of computing the relative entropy from two .mod files, just use the specified value.  The .mod files aren't required in this case.

**--LminH**, **-L** \<value\> \[or **--NH**/-N, for backward compatibility\]

-

  Report the expected length that would produce the specified value of L\_min \* H (i.e., the specified PIT), assuming H remains constant (it generally won't).  Can be used iteratively to converge on a desired PIT.

**--help**, **-h**

-

  Print this help message.

### NOTE:

-

  The relative entropy is currently computed by brute force, i.e., by enumerating all possible labelings of the leaves of the tree. This approach won't be feasible with large trees.