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/cons_test/ctl/baseml.ctl

http://github.com/sbotond/phylosim
Visual Basic | 34 lines | 27 code | 7 blank | 0 comment | 1 complexity | 20beece5690aceba1bc2736ad6137939 MD5 | raw file
 1      seqfile = sim.phy
 2     treefile = ../tree/test_tree.t
 3
 4      outfile = mlb       * main result file
 5        noisy = 0   * 0,1,2,3: 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 
 9
10        model = 3   * 0:JC69, 1:K80, 2:F81, 3:F84, 4:HKY85
11                    * 5:T92, 6:TN93, 7:REV, 8:UNREST, 9:REVu; 10:UNRESTu
12
13        Mgene = 0   * 0:rates, 1:separate; 2:diff pi, 3:diff kapa, 4:all diff
14
15*        ndata = 100
16        clock = 0   * 0:no clock, 1:clock; 2:local clock; 3:CombinedAnalysis
17    fix_kappa = 0   * 0: estimate kappa; 1: fix kappa at value below
18        kappa = 5  * initial or fixed kappa
19
20    fix_alpha = 0   * 0: estimate alpha; 1: fix alpha at value below
21        alpha = 1   * initial or fixed alpha, 0:infinity (constant rate)
22       Malpha = 0   * 1: different alpha's for genes, 0: one alpha
23        ncatG = 8   * # of categories in the dG, AdG, or nparK models of rates
24        nparK = 0   * rate-class models. 1:rK, 2:rK&fK, 3:rK&MK(1/K), 4:rK&MK 
25
26        nhomo = 0   * 0 & 1: homogeneous, 2: kappa for branches, 3: N1, 4: N2
27        getSE = 0   * 0: don't want them, 1: want S.E.s of estimates
28 RateAncestor = 0   * (0,1,2): rates (alpha>0) or ancestral states
29
30   Small_Diff = 7e-6
31    cleandata = 1  * remove sites with ambiguity data (1:yes, 0:no)?
32*        icode = 0  * (with RateAncestor=1. try "GC" in data,model=4,Mgene=4)
33*  fix_blength = -1  * 0: ignore, -1: random, 1: initial, 2: fixed
34       method = 0  * Optimization method 0: simultaneous; 1: one branch a time