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0 * 0: paml format (mc.paml); 1:paup format (mc.nex)
1234567 * random number seed (odd number)
50 10000 100 * <# seqs> <# nucleotide sites> <# replicates>
0.1 0.2 0.3 1.5 * birth rate, death rate, sampling fraction, and mutation rate (tree height)
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
//end of file
==================================================
The rest of this data file are notes, ignored by 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 !! =====
A few interesting trees:
For TipDate models:
((A@1970: 0.3, B@1990: 0.5) @1940 :0.4, (C@1940 : 0.1, (D@1960: 0.1, (E@1980:0.1, F@2000: 0.3) @1970 :0.2) @1950 : 0.2) @1930 :0.3) @1900;
(((A :0.1, B :0.2) :0.12, C :0.3) :0.123, D :0.4, E :0.5) ;
(((human: 0.1, chimpanzee: 0.1): 0.1, gorilla: 0.2): 0.1, orangutan: 0.3);
((a:0.1, b:0.2):0.12, (c:0.3, d:0.4):0.34, ((e:0.5, f:0.6):0.56, (g:0.7, h:0.8):0.78):0.69);
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