seqfile = examples/mtprim9.nuc * sequence data file name
    outfile = mp        * main result file
   treefile = examples/9s.trees  * tree structure file name

    seqtype = 0  * 0:nucleotides; 2:amino acids, 3:binary
      ncatG = 8  * # of categories in the dG model of rates
      nhomo = 0  * nonhomogeneous in calcualting P for branch