consEntropy(1)
For use with phastCons. Given phylogenetic models for conserved and
Description
CONSENTROPY
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.