consEntropy - For use with phastCons. Given phylogenetic models
for conserved and
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).
consEntropy [OPTIONS] <target-coverage>
<expected-length> \
- [ <cons.mod> <noncons.mod> ]
--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.
- 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.