new_contents: #!/opt/anaconda3/bin/python3.4
  import sys
  import re
  
  if (len(sys.argv) != 2):
      print("GC_content <phylip>")
      sys.exit(0)
  
  file  = sys.argv[1]
  
  def compute_missingdata(phylip):
      f = open(phylip,"r")
      lines = f.readlines()
      f.close()
      lines_clean = []
      Nsite_nuc = 0
      for line,index in zip(lines,[i for i in range(0,len(lines))]):
          if(index != 0):
              lines_clean.append(line.split(" ")[-1])
          else:
              Nsite_nuc = int(line.split(" ")[-1].strip())
  
      missing = Nsp = Nchar = 0
      for line_clean in lines_clean:
          line_clean = line_clean.strip()
          Nsp += 1
          lenth = len(line_clean)
          missing += len(re.findall("[Xx\-\?]",str([line_clean[i] for i in range(0,lenth)])))
          Nchar += len(re.findall("[ACGTacgtXx\-\?]",str([line_clean[i] for i in range(0,lenth)])))
      return (missing/(Nsp*Nsite_nuc),Nsp,Nsite_nuc,Nchar)
  
  tup = compute_missingdata(file)
  print("Ntaxa ", tup[1], " Nsite_nuc ", tup[2], " Nnuc[ACGTacgt-?] ",tup[3])
  print("percent missing data ", round(tup[0],3))
subject: add computation of the missing data "rought"