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.