- Modified <genesmith.cpp> to selectively process HMMER scores
- added subroutines to <hmmgen_gene.pl> and <hmmgen_branch.pl>
  allowing them to switch between training emission with/without
  pseudo counting
- Created <run_gs_hmmer_eval.pl> wrapper specifically for generating
  predictions that use HMMER/SW-alignment scores
  * generates predictions one gene at a time (for now)