#### /cons_test/ctl/baseml.ctl

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