seqfile = lysinYangSwanson2002.nuc
treefile = lysin.trees
outfile = mlc * main result file name
noisy = 3 * 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 = 1 * 1:codons; 2:AAs; 3:codons-->AAs
CodonFreq = 2 * 0:1/61 each, 1:F1X4, 2:F3X4, 3:codon table
model = 0 * codonml: 0:one, 1:b, 2:2 or more dN/dS ratios for branches
NSsites = 0 * 0:one w;1:neutral;2:positive; 3:discrete;4:freqs;
* 5:gamma;6:2gamma;7:beta;8:beta&w;9:betaγ
* 10:beta&1+gamma; 11:beta&1>normal; 12:0&2normal; 13:3normal
icode = 0 * 0:standard genetic code; 1:mammalian mt; 2-10:see below
Mgene = 0 * codonml: 0:rates, 1:separate; 2:diff pi, 3:diff kapa, 4:all diff
fix_kappa = 0 * 1: kappa fixed, 0: kappa to be estimated
kappa = 1.6 * initial or fixed kappa
fix_omega = 0 * 1: omega or omega_1 fixed, 0: estimate
omega = .8 * initial or fixed omega, for codons or codon-based AAs
ncatG = 3 * # of categories in dG of NSsites models
getSE = 0 * 0: don't want them, 1: want S.E.s of estimates
Small_Diff = 3e-7
cleandata = 0 * remove sites with ambiguity data (1:yes, 0:no)?
method = 0 * 0: simultaneous; 1: one branch at a time