seqfile = mhc.phy treefile = mhc.tre outfile = mhc.free * main result file name noisy = 9 * 0,1,2,3,9: how much rubbish on the screen verbose = 0 * 0: concise; 1: detailed, 2: too much runmode = 0 * 0: user tree; 1: semi-automatic; 2: automatic * 3: StepwiseAddition; (4,5):PerturbationNNI; -2: pairwise seqtype = 1 * 1:codons; 2:AAs; 3:codons-->AAs CodonFreq = 3 * 0:1/61 each, 1:F1X4, 2:F3X4, 3:codon table aaDist = 0 * 0:equal, +:geometric; -:linear, 1-6:G1974,Miyata,c,p,v,a model = 1 * 0:one, 1:b, 2:2 or more dN/dS ratios for branches NSsites = 0 * 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 Mgene = 0 * 0:rates, 1:separate; 2:diff pi, 3:diff kapa, 4:all diff 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 = .5 * initial or fixed omega, for codons 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 = 1 * # of categories in dG of NSsites models clock = 0 * 0:no clock, 1:global clock; 2:local clock; 3:TipDate 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) * Genetic codes: 0:universal, 1:mammalian mt., 2:yeast mt., 3:mold mt., * 4: invertebrate mt., 5: ciliate nuclear, 6: echinoderm mt., * 7: euplotid mt., 8: alternative yeast nu. 9: ascidian mt., * 10: blepharisma nu. * These codes correspond to transl_table 1 to 11 of GENEBANK. * Small_Diff = .5e-6 cleandata = 0 * remove sites with ambiguity data (1:yes, 0:no)? * ndata = 4 * fix_blength = -1 * 0: ignore, -1: random, 1: initial, 2: fixed method = 0 * 0: simultaneous; 1: one branch at a time