Workflow.txt

For each matrix:

  Classify each ontogenetically depedent character as neomorphic or transformational [big job]
    Create text file for each matrix, listing N or T for each character in turn
  
  Copy matrix, replacing neomorphic/transformational inapplicables with: [perl - easy]
    
    1a. ?/?  - ambiguous
    1b. 0/?  - ambigAbsent
             
    2.  0/9  - extraState
             
    3.  0/-  - inapplicable
    
  Cases 1a, 1b, 2: [ do in the above perl script ]
  
    Conduct comprehensive TNT search
    
  Case 3: [ Probably do one by one in R, to supervise completion ]
          [ Get this going before TNT searches - it'll need longer to run ]
    
    Conduct comprehensive tree search in R::inapplicable
    Calculate scores of optimal trees from cases 1a, 1b, 2
    
  Read all MPTs by all methods into R
  
  For each tree,   
    Determine whether it's an MPT under each method
    
  Draw Venn Diagram showing size and overlap of MPT islands between methods.
  Can we use quartet distance instead of RF, please?