seqfile = ENSGT00390000005194.Euteleostomi.001.phy * sequence data file name
treefile = ENSGT00390000005194.Euteleostomi.001.034.nwk * tree structure file name
outfile = ENSGT00390000005194.Euteleostomi.001.034.H1.mlc * main result file name
noisy = 0 * 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
ndata = 1 * specifies the number of separate data sets in the file
clock = 0 * 0: no clock, unrooted tree, 1: clock, rooted tree
aaDist = 0 * 0:equal, +:geometric; -:linear, 1-6:G1974,Miyata,c,p,v,a
* 7:AAClasses
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 = 2 * 0:one w; 1:neutral; 2:positive 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 = 2.05154 * 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
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 * small value used in the difference approximation of derivatives
cleandata = 0 * remove sites with ambiguity data (1:yes, 0:no)?
fix_blength = 1 * 0: ignore, -1: random, 1: initial, 2: fixed
method = 0 * 0: simultaneous; 1: one branch at a time