Rebuilt HMM training process
- New Code
    - Emission Training
	  <run_hmmgen.pl>
	  <hmmgen_gene.pl> -> trains emissions for all states
	                       other than branch states
	  <hmmgen_branch.pl> -> only trains branch state emissions
	- HMM generation
	  <hmm_assmbl.pl> -> trains transition probabilities and
	                     uses trained emissions along with user
	                     input to generate HMM model file
	- Wrapper Script
	  <run_gs_eval.pl> -> Runs through the entire process of
	                      splitting the input data and generating
	                      a gene predictions using 5 fold cross
	                      validation (outputs files necessary for
	                      <evaluator.pl>)
- Modified existing code to to adjust to training format