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.

consEntropy 1.4                                     May 2016                                      CONSENTROPY(1)