seqfile = aga2aa.seq
treefile = aga2.tre

outfile = aga2aa.mlc * 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 = 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
aaRatefile = mtmam.dat * only used for aa seqs with model=empirical(_F)
* dayhoff.dat, jones.dat, wag.dat, mtmam.dat, or your own

model = 3
* models for AAs or codon-translated AAs:
* 0:poisson, 1:proportional, 2:Empirical, 3:Empirical+F
* 6:FromCodon, 7:AAClasses, 8:REVaa_0, 9:REVaa(nr=189)

icode = 1 * 0:universal code; 1:mammalian mt; 2-10:see below
Mgene = 0
* codon: 0:rates, 1:separate; 2:diff pi, 3:diff kappa, 4:all diff
* AA: 0:rates, 1:separate

clock = 0 * 0:no clock, 1:global clock; 2:local clock

fix_kappa = 0 * 1: kappa fixed, 0: kappa to be estimated
kappa = 1.234567 * initial or fixed kappa
fix_omega = 0 * 1: omega or omega_1 fixed, 0: estimate
omega = 1.414 * initial or fixed omega, for codons or codon-based AAs

fix_alpha = 0 * 0: estimate gamma shape parameter; 1: fix it at alpha
alpha = 0.3 * initial or fixed alpha, 0:infinity (constant rate)
Malpha = 0 * different alphas for genes
ncatG = 8 * # of categories in dG of NSsites models

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 = -1 * 0: ignore, -1: random, 1: initial, 2: fixed
method = 1 * 0: simultaneous; 1: one branch at a time