.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.4.
.TH CONSENTROPY "1" "May 2016" "consEntropy 1.4" "User Commands"
.SH NAME
consEntropy \- For use with phastCons.  Given phylogenetic models for conserved and
.SH DESCRIPTION
For use with phastCons.
Given phylogenetic models for conserved and
.IP
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 \fB\-\-LminH\fR).
.SH SYNOPSIS
consEntropy [OPTIONS] <target\-coverage> <expected\-length> \e
.IP
[ <cons.mod> <noncons.mod> ]
.SH OPTIONS
.HP
\fB\-\-H\fR, \fB\-H\fR <value>
.IP
Instead of computing the relative entropy from two .mod files,
just use the specified value.  The .mod files aren't required
in this case.
.HP
\fB\-\-LminH\fR, \fB\-L\fR <value> [or \fB\-\-NH\fR/\-N, for backward compatibility]
.IP
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.
.HP
\fB\-\-help\fR, \fB\-h\fR
.IP
Print this help message.
.SS "NOTE:"
.IP
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.