1 1     * 0,1:seqs or patterns in paml format (mc.paml); 2:paup format (mc.nex); 3: paup JC69 format
2 -123  * random number seed (odd number)
3
45 895 100  * <# seqs>  <# nucleotide sites>  <# replicates>
5-1         * <tree length, use -1 if tree below has absolute branch lengths>
6
7((Human: 0.056647, Chimpanzee: 0.071554): 0.028080, Gorilla: 0.075518, (Orangutan: 0.259783, Gibbon: 0.400727): 0.100618);
8
97          * model: 0:JC69, 1:K80, 2:F81, 3:F84, 4:HKY85, 5:T92, 6:TN93, 7:REV
100.88892  0.03190  0.00001  0.07102  0.02418 * kappa or rate parameters in model
110.2500  5     * <alpha>  <#categories for discrete gamma>
12
130.25318  0.32894  0.31196  0.10592    * base frequencies
14  T        C        A        G
15
16
17==================================================
18The rest of this data file are notes, ignored by the program evolver.
19Change the values of the parameters, but do not delete them.
20evolver simulates nucleotide sequences under the REV+Gamma model
21and its simpler forms.
22
23More notes:
24  Parameter kappa or rate parameters in the substituton model:
25    For TN93, two kappa values are required, while for REV, 5 values
26    (a,b,c,d,e) are required (see Yang 1994 for the definition of these
27    parameters).
28    The kappa parameter is defined differently under HKY85 (when k=1 means
29    no transition bias) and under F84 (when k=0 means no bias).
30    JC69 and F81 are considered species cases of HKY85, so use 1 for kappa
31    for those two models.  Notation is from my two papers in JME in 1994.
32
33  Use equal base frequencies (0.25) for JC69 and K80.
34  Use 0 for alpha to have the same rate for all sites.
35  Use 0 for <#categories for discrete gamma> to use the continuous gamma
36
37=========!! Check screen output carefully !! =====
38