practice2.txt

      seqfile = uniquegenename.pr.phy * sequence data filename
     treefile = speciesTree.tre    * tree structure file name

      outfile = uniquegenename.paml           * 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 = 4  * 0: user tree;  1: semi-automatic;  2: automatic
                   * 3: StepwiseAddition; (4,5):PerturbationNNI; -2: pairwise

      seqtype = 2  * 1:codons; 2:AAs; 3:codons-->AAs
   aaRatefile = /data/paml4.8/dat/wag.dat * only used for aa seqs with model=empirical(_F)
                   * dayhoff.dat, jones.dat, wag.dat, mtmam.dat, or your own

        model = 3  * 0:poisson, 1:proportional, 2:Empirical, 3:Empirical+F
                   * 6:FromCodon, 7:AAClasses, 8:REVaa_0, 9:REVaa(nr=189)
        Mgene = 1  * aaml: 0:rates, 1:separate; 

    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 = 2  * # 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 = 1 * (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 = 2
        method = 0   * 0: simultaneous; 1: one branch at a time