codeml.ctl

seqfile = codon.phy * sequence data file name
treefile = tree.phy * tree structure file name
outfile = test.mlc * main result file name

noisy = 9 * 0,1,2,3,9: how much rubbish on the screen
verbose = 1 * 1: detailed output, 0: concise output
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 = 2 * 0:1/61 each, 1:F1X4, 2:F3X4, 3:codon table
clock = 0 * 0: no clock, unrooted tree, 1: clock, rooted tree
aaDist = 0 * 0:equal, +:geometric; -:linear, {1-5:G1974,Miyata,c,p,v}
model = 0

NSsites = 0
* 0:one w; 1:NearlyNeutral; 2:PositiveSelection; 3:discrete;
* 4:freqs; 5:gamma;6:2gamma;7:beta;8:beta&w;9:betaγ10:3normal
icode = 0 * 0:standard genetic code; 1:mammalian mt; 2-10:see below
Mgene = 0 * 0:rates, 1:separate; 2:pi, 3:kappa, 4:all

fix_kappa = 0 * 1: kappa fixed, 0: kappa to be estimated
kappa = 1 * initial or fixed kappa
fix_omega = 0 * 1: omega or omega_1 fixed, 0: estimate
omega = 1 * initial or fixed omega, for codons or codon-based AAs
ncatG = 10 * # of categories in the dG or AdG models of rates

getSE = 1 * 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 = .45e-6
cleandata = 1 * remove sites with ambiguity data (1:yes, 0:no)?
fix_blength = 0 * 0: ignore, -1: random, 1: initial, 2: fixed