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] <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.