0          * 0:paml format (mc.paml); 1:paup format (mc.paup)
21234567   * random number seed (odd number)

4 10000 1  * <# seqs>  <# nucleotide sites>  <# replicates>
-1         * <tree length, use -1 if tree has absolute branch lengths>

((human :0.1, chimpanzee :0.1) :0.12, gorilla :0.22, orangutan :0.4);

7          * model: 0:JC69, 1:K80, 2:F81, 3:F84, 4:HKY85, 5:T92, 6:TN93, 7:REV
10 5 1 2 3 * kappa or rate parameters in model
0.5  4     * <alpha>  <#categories for discrete gamma>

0.1 0.2 0.3 0.4    * base frequencies
  T   C   A   G


==================================================
The rest of this data file are notes, ignored by the program evolver.
Change the values of the parameters, but do not delete them.
evolver simulates nucleotide sequences under the REV+Gamma model
and its simpler forms.

More notes:
  Parameter kappa or rate parameters in the substituton model: 
    For TN93, two kappa values are required, while for REV, 5 values
    (a,b,c,d,e) are required (see Yang 1994 for the definition of these
    parameters).  
    The kappa parameter is defined differently under HKY85 (when k=1 means
    no transition bias) and under F84 (when k=0 means no bias).
    JC69 and F81 are considered species cases of HKY85, so use 1 for kappa
    for those two models.  Notation is from my two papers in JME in 1994.
  
  Use equal base frequencies (0.25) for JC69 and K80.
  Use 0 for alpha to have the same rate for all sites.
  Use 0 for <#categories for discrete gamma> to use the continuous gamma

=========!! Check screen output carefully !! =====
