seqfile = Seq_ATP1A1.txt * sequence data filename treefile = BranchSite_BranchD.trees * tree structure file name outfile = Branch_Site_Model_A,BranchD,selection * main result file name noisy = 9 * 0,1,2,3,9: how much rubbish on the screen verbose = 0 runmode = 0 seqtype = 1 * 1:codons; 2:AAs; 3:codons-->AAs CodonFreq = 2 * 0:1/61 each, 1:F1X4, 2:F3X4, 3:codon table clock = 0 * 0:no clock, 1:global clock; 2:local clock; 3:TipDate aaDist = 0 * 0:equal, +:geometric; -:linear, 1-6:G1974,Miyata,c,p,v,a aaRatefile = /../wag.dat model = 2 * models for codons: * 0:one, 1:b, 2:2 or more dN/dS ratios for branches NSsites = 2 * 0:one w;1:neutral;2:selection; 3:discrete;4:freqs; * 5:gamma;6:2gamma;7:beta;8:beta&w;9:betaγ * 10:beta&gamma+1; 11:beta&normal>1; 12:0&2normal>1; * 13:3normal>0 icode = 0 * 0:universal code; 1:mammalian mt; 2-10:see below fix_kappa = 0 * 1: kappa fixed, 0: kappa to be estimated kappa = 3 * initial or fixed kappa fix_omega = 0 * 1: omega or omega_1 fixed, 0: estimate omega = 1.5 * initial or fixed omega, for codons or codon-based AAs fix_alpha = 1 * 0: estimate gamma shape parameter; 1: fix it at alpha alpha = 0 * initial or fixed alpha, 0:infinity (constant rate) Malpha = 0 * different alphas for genes ncatG = 10 * # of categories in dG of NSsites models. The variable ncatG is ignored by the program, since the number of site classes is fixed under both models A and B. getSE = 0 * 0: don't want them, 1: want S.E.s of estimates RateAncestor = 0 * (0,1,2): rates (alpha>0) or ancestral states (1 or 2) Small_Diff = .5e-6 * cleandata = 1 * method = 1 * 0: simultaneous; 1: one branch at a time #This control file is from lysozymeLarge.ctl which specifies the branch-site modelA, the alternative hypothesis #Here are specifications to implement both the #null and alternative hypotheses. See Zhang et al. (2005; table 5). # # #Null hypothesis (branch site model A, with w2 = 1 fixed): # model = 2 NSsites = 2 fix_omega = 1 omega = 1 # # #Alternative hypothesis (branch site model A, with w2 estimated): # model = 2 NSsites = 2 fix_omega = 0 omega = 1.5 (or any value > 1)