code: def run_treefix(input, stree_file, smap_file, a_ext=".fasta", \
                  o_ext=".dnd", n_ext = ".treefix.dnd", **kwargs):
      
      cl = TreeFixCommandline(input=input, \
              stree_file=stree_file, smap_file=smap_file, a_ext=a_ext, \
              o=o_ext, n=n_ext, **kwargs)
      outtreefile = input.rsplit(o_ext, 1)[0] + n_ext
      print("TreeFix:", cl, file=sys.stderr)
      r, e = cl.run()
  
      if e:
          print("***TreeFix could not run", file=sys.stderr)
          return None
      else:
          logging.debug("new tree written to {0}".format(outtreefile))
          return outtreefile
docs: get the ML tree closest to the species tree