TO DO:
- max parsimony ratchet needs to be multi-threaded




Directory Structure of logos:
	  - PAUP    
	  Paup working directory
	  - PAUPRat 
	  Pauprat working directory
	  -Perl
	  Old and unused perl scripts
	  -Simulator
	  Simulator working directory
	  -logs
	  Log directory - not sure who uses it
	  -r8s 
	  R8s working directory

Public Perl scripts to use simulator.
- makeExperiment.pl
- generate_r8s.pl
- r8s2logos.pl
- logos2PAUP.pl

Public Perl scripts to analyze the results.
- makeDistances.pl
- makeDupTrees.pl
- makeScores.pl
- makeTrueTree.pl

Private Perl scripts necessary for the simulation
- comp_distf.pl computes distance matrices for NJ and UPGMA
- generate_PAUP.pl generates the PAUP files
- generate_PAUPRat.pl generates the PAUPRat file
- generate_logos.pl takes a r8s file and generates a logos file
- wrap_tds.pl

Chain of calls to perl scripts:
makeExperiment with parameters:
	       suffix param dir
	       n, u, ht, k, h, i
	       copies all result files into the same directory 	       
	       
	       generate_r8s.pl n, 1.0, "ultra" 
				 produces
			          "r8s_$suffix_$param_out.tree"
				 calls
			r8s/bin/r8s -b -f
				       reads
				        "r8s_$suffix_$param_in.tree"
				       produces
					"r8s_$suffix_$param_out.tree"


	       r8s2logos.pl	 k, u, ht, h
				 reads
				  "r8s_$suffix_$param_out.tree"
				 produces
				  "logos_$suffix_$param_out.nex"
				 calls
			generate_logos.pl k, u, ht, h
			#primary function is to convert
			#k, u, ht, h into 
			#logos rates parameters
					reads
					 "r8s_$suffix_$param_out.tree"
					produces
					 "logos_$suffix_$param_in.nex"
			java Simulator
					reads 
					 "logos_$suffix_$param_in.nex"
					produces
					 "logos_$suffix_$param_out.nex"

	       logos2PAUP.pl k $method 
				 reads
				  "logos_$suffix_$param_out.nex"
				 produces
				  "PAUP_$suffix_$param_$method_out.$type"
				 where $type = [trees | scores | cons]
				 calls
			generate_PAUP.pl k $method
				    reads
				     "logos_$suffix_$param_out.nex"
				    produces
				     "PAUP_$suffix_$param_$method_in.nex"
			PAUP/paup -n
				    reads 
				     "PAUP_$suffix_$param_$method_in.nex"
				    produces
				     "PAUP_$suffix_$param_$method_out.$type"
				    where $type = [trees | scores | cons]
			generate_PAUPRat nchar nreps pct
				    produces
				     "PAUPRat_$suffix_$param_mpr_in.nex"
			PAUPRat/pauprat 
				    reads 
				     "PAUPRat_$suffix_$param_mpr_in.nex"
				    produces
				     "PAUPRat_$suffix_$param_mpr_out.trees"
				     "PAUPRat_$suffix_$param_mpr_out.scores"

#makeTrueTree is
#NO LONGER NECESSARY since TDS does not work!
makeTrueTree $suffix $param $dir
	     reads	     
	      "$dir/logos_$suffix_$param_out.nex"
	     produces 
	      "$dir/result_$suffix_$param_truetree"
	      A file with the true tree in it (not a nexus file)
	      Optional (not implemented):
	      "$dir/result_$suffix_$param_truetree.nex"
	      A file with the true tree in it (nexus format)

makeScores $suffix $param $dir
	     reads
	      "$dir/result_$suffix_$param_$method_trees.nex"
	     produces 
	      "$dir/result_$suffix_$param_$method_scores"
	      reports for each tree in the result tree file
	      for each tree HI and RC if applicable as
	      well as fp, fn, symdiff score results.

makeDistances $suffix $param $dir
	     produces
	      "$dir/result_$suffix_$param_$method_distances.nex"
	      report with for each tree in result tree file
	      distance to tree #1:
	      fp - fn - # interior edges - fp rate - fn rate - symdiff rate

makeDupTrees $suffix $param $dir $method
	     produces 
	      "$dir/result_$suffix_$param_$method_trees.nex"
	      A file with all the result trees for all 
	      methods ?
	      ModelTree 1 tree for all methods
	      MutationTree 1 tree for all methods
	      TrueTree 1 tree for all methods
	      NJ       1 tree for NJ
	      UPGMA    1 tree for UPGMA
	      MP       100 or optimal scored trees for MP
	      MPR      nreps or optimal trees for MPR
	      MPU      nreps or optimal trees for MPU
	     
makeTrees 
	  same as makeDupTrees but eliminates duplicates
	  produced by parsimony method. Tree #1, 2, 3
	  may still be duplicates.	      
	  Duplicates are identified by symdiff from the
	  scores file.
	  Duplicates are eliminated by PAUP already - which
	  makes this script un-necessary.