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追梦人生123金虫 (小有名气)
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[求助]
用PAM做L正选择时候参数设置应注意的问题？
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PAML在做正选择的时候，各种参数应该怎么设置啊？像下面的这个例子，希望得到大家的帮助，万分感谢啊！！！ seqfile =Ppfulllength.nuc * sequence data filename treefile =Ppfulllength.trees * tree structure file name outfile =Ppfulllength.out * main result file name noisy = 9 * 0,1,2,3,9: how much rubbish on the screen verbose = 1 * 0: concise; 1: detailed, 2: too much runmode = 0 * 0: user tree; 1: semi-automatic; 2: automatic * 3: StepwiseAddition; (4,5)  erturbationNNI; -2: pairwiseseqtype = 1 * 1:codons; 2:AAs; 3:codons-->AAs CodonFreq = 2 * 0:1/61 each, 1:F1X4, 2:F3X4, 3:codon table * ndata = 10 clock = 0 * 0:no clock, 1:clock; 2:local clock; 3:CombinedAnalysis aaDist = 0 * 0:equal, +:geometric; -:linear, 1-6:G1974,Miyata,c,p,v,a aaRatefile = dat/jones.dat * only used for aa seqs with model=empirical(_F) * dayhoff.dat, jones.dat, wag.dat, mtmam.dat, or your own model = 0 * models for codons: * 0  ne, 1:b, 2:2 or more dN/dS ratios for branches* models for AAs or codon-translated AAs: * 0:poisson, 1:proportional, 2:Empirical, 3:Empirical+F * 6:FromCodon, 7:AAClasses, 8:REVaa_0, 9:REVaa(nr=189) NSsites = 0 3 7 8 * 0 ne 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 * codon: 0:rates, 1:separate; 2:diff pi, 3:diff kapa, 4:all diff * AA: 0:rates, 1:separate 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 = .4 * 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 = 8 * # of categories in dG of NSsites models getSE = 0 * 0: don't want them, 1: want S.E.s of estimates RateAncestor = 1 * (0,1,2): rates (alpha>0) or ancestral states (1 or 2) Small_Diff = .5e-6 cleandata = 1 * remove sites with ambiguity data (1:yes, 0:no)? * fix_blength = -1 * 0: ignore, -1: random, 1: initial, 2: fixed method = 0 * Optimization method 0: simultaneous; 1: one branch a time * 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. |
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