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