seqfile = Seq_ATP1A1.txt treefile = BranchModel_BranchD.trees outfile = ATP1A-BranchD,selection,36sp noisy = 9 * 0,1,2,3,9: how much rubbish on the screen verbose = 1 * 1: detailed output, 0: concise output runmode = 0 * 0: user tree; 1: semi-automatic; 2: automatic * 3: StepwiseAddition; (4,5):PerturbationNNI seqtype = 1 * 1:codons; 2:AAs; 3:codons-->AAs CodonFreq = 2 * 0:1/61 each, 1:F1X4, 2:F3X4, 3:codon table model = 2 * models for codons: * 0:one, 1:b, 2:2 or more dN/dS ratios for branches NSsites = 0 * dN/dS among sites. 0:no variation, 1:neutral, 2:positive icode = 0 * 0:standard genetic code; 1:mammalian mt; 2-10:see below fix_kappa = 0 * 1: kappa fixed, 0: kappa to be estimated kappa = 2 * initial or fixed kappa fix_omega = 0 * 1: omega or omega_1 fixed, 0: estimate omega = 1 * initial or fixed omega, for codons or codon-transltd 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 = 4 * # of categories in the dG or AdG models of rates clock = 0 * 0: no clock, unrooted tree, 1: clock, rooted tree getSE = 0 * 0: don't want them, 1: want S.E.s of estimates RateAncestor = 0 * (1/0): rates (alpha>0) or ancestral states (alpha=0) method = 0 * 0: simultaneous; 1: one branch at a time fix_blength = 0 * 0: ignore, -1: random, 1: initial, 2: fixed * Free-ratio model