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.