/cons_test/ctl/codeml_codon.ctl

 1      seqfile = sim.phy			* sequence data file name
 2     treefile = ../tree/test_tree.t	* tree structure file name
 3
 4      outfile = mlc          * main result file name
 5        noisy = 0   * 0,1,2,3,9: how much rubbish on the screen
 6      verbose = 0   * 1: detailed output, 0: concise output
 7      runmode = 0   * 0: user tree;  1: semi-automatic;  2: automatic
 8                    * 3: StepwiseAddition; (4,5):PerturbationNNI; -2: pairwise
 9
10      seqtype = 1   * 1:codons; 2:AAs; 3:codons-->AAs
11    CodonFreq = 2   * 0:1/61 each, 1:F1X4, 2:F3X4, 3:codon table
12        clock = 0   * 0: no clock, unrooted tree, 1: clock, rooted tree
13       aaDist = 0   * 0:equal, +:geometric; -:linear, {1-5:G1974,Miyata,c,p,v}
14        model = 0
15
16      NSsites = 0
17                    * 0:one w; 1:NearlyNeutral; 2:PositiveSelection; 3:discrete;
18                    * 4:freqs; 5:gamma;6:2gamma;7:beta;8:beta&w;9:betaγ10:3normal
19        icode = 0   * 0:standard genetic code; 1:mammalian mt; 2-10:see below
20        Mgene = 0   * 0:rates, 1:separate; 2:pi, 3:kappa, 4:all
21
22    fix_kappa = 0   * 1: kappa fixed, 0: kappa to be estimated
23        kappa = .3   * initial or fixed kappa
24    fix_omega = 0   * 1: omega or omega_1 fixed, 0: estimate 
25        omega = 1.3  * initial or fixed omega, for codons or codon-based AAs
26        ncatG = 8   * # of categories in the dG or AdG models of rates
27
28        getSE = 0   * 0: don't want them, 1: want S.E.s of estimates
29 RateAncestor = 0   * (0,1,2): rates (alpha>0) or ancestral states (1 or 2)
30
31   Small_Diff = .45e-6
32    cleandata = 1  * remove sites with ambiguity data (1:yes, 0:no)?
33  fix_blength = 0  * 0: ignore, -1: random, 1: initial, 2: fixed