CODEML sample control file

Sample CODEML control file


seqfile = stewart.aa * sequence data file name
outfile = mlc * main result file name
treefile = stewart.trees * tree structure file name
noisy = 9 * 0,1,2,3,9: how much rubbish on the screen
verbose = 0 * 1: detailed output, 0: concise output
runmode = 0 * 0: user tree; 1: semi-automatic; 2: automatic
* 3: StepwiseAddition; (4,5):PerturbationNNI; -2: pairwise
seqtype = 2 * 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:TipDate
aaDist = 0 * 0:equal, +:geometric; -:linear, 1-6:G1974,Miyata,c,p,v,a
* 7:AAClasses
aaRatefile = wag.dat * only used for aa seqs with model=empirical(_F)
* dayhoff.dat, jones.dat, wag.dat, mtmam.dat, or your own
model = 2
* models for codons:
* 0:one, 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, 8:REVaa_0, 9:REVaa(nr=189)
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; 2-11:see below
Mgene = 0 * 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 = 3 * # of categories in dG of NSsites models
fix_rho = 1 * 0: estimate rho; 1: fix it at rho
rho = 0. * initial or fixed rho, 0:no correlation
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)
Small_Diff = .5e-6
* cleandata = 0 * remove sites with ambiguity data (1:yes, 0:no)?
* fix_blength = 0 * 0: ignore, -1: random, 1: initial, 2: fixed
method = 0 * 0: simultaneous; 1: one branch at a time

The variables seqfile, outfile, treefile, noisy, Mgene, fix_alpha, alpha, Malpha, fix_rho, rho, clock, getSE, RateAncestor, Small_Diff, cleandata, ndata, fix_blength, and method are used in the same way as in baseml.ctl and are described in the previous section. The variable seqtype specifies the type of sequences in the data; seqtype = 1 means codon sequences (the program is then codonml); 2 means amino acid sequences (the program is then aaml); and 3 means codon sequences which are to be translated into proteins for analysis.