PROGRAM: consEntropy
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).
USAGE: consEntropy [OPTIONS] \
[ ]
OPTIONS:
--H, -H
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 [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.