- Revised all training scripts so they would efficiently
  train all possible emission for both standard (3 CDS states)
  and basic (1 CDS state) models
    - hmmgen_gene.pl
    - hmmgen_branch.pl
    - hmm_assmbl.pl
    - run_hmmgen.pl
- Modified print statement in <genesmith.cpp> to account for these
  changes