/* Which Model to use? */
modelinf.gene1
L  /* How much output? Options: L = Loud mode (prints more output, the 
      default), Q = Quiet mode (prints less output - use with parametric 
      bootstrap) */
D  /* Predict Secondary Structure? Options: P= predict, D = do not predict
      (the default option) */
N  /* Does user tree specify names (N) or specify order (O) of sequences
      in sequence data file? */
   /* The topology is in the file listed below*/
finaltree
   /* End of hmmcntrl.dat */