code: def _getarray(loci, snames):
      
      ## make an empty matrix
      lxs = np.zeros((len(snames), len(loci)), dtype=np.uint64)
  
      ## fill the matrix
      for loc in xrange(len(loci)):
          for seq in loci[loc].split("\n"):
              if "//" not in seq:
                  lxs[snames.index(seq.split()[0][:]), loc] += 1
  
      return lxs, snames
docs: parse loci list and return presence/absence matrix
      ordered by the tips on the tree or list of names.