24小时热门版块排行榜

返回列表

追梦人生123

金虫 (小有名气)

应助: 1 (幼儿园)
金币: 1344.2
散金: 1
红花: 1
帖子: 154
在线: 72.5小时
虫号: 2185211
注册: 2012-12-13
专业: 微生物生理与生物化学

[求助] 用PAM做L正选择时候参数设置应注意的问题？

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: pairwise

   seqtype = 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.

回复此楼