seqfile = mtCDNAape.txt
treefile = mtCDNAape.trees
outfile = mlc * main result file name
noisy = 3 * 0,1,2,3,9: how much rubbish on the screen
verbose = 0 * 0: concise; 1: detailed, 2: too much
runmode = 0
seqtype = 1 * 1:codons; 2:AAs; 3:codons-->AAs
CodonFreq = 2 * 0:1/61 each, 1:F1X4, 2:F3X4, 3:codon table
* 4:F1x4MG, 5:F3x4MG, 6:FMutSel3x4, 7:FMutSelCodon
clock = 0 * 0:no clock, 1:global clock; 2:local clock
aaDist = 7 * 0:equal, +:geometric; -:linear, 1-6:G1974,Miyata,c,p,v,a
aaRatefile = ../../dat/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
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 = 1 * 0:universal 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 = 1.234567 * 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 = 1 * 0: estimate gamma shape parameter; 1: fix it at alpha
alpha = 0. * initial or fixed alpha, 0:infinity (constant rate)
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 = .5e-6
* cleandata = 0 * remove sites with ambiguity data (1:yes, 0:no)?
* ndata = 10
* fix_blength = -1 * 0: ignore, -1: random, 1: initial, 2: fixed
method = 0 * 0: simultaneous; 1: one branch at a time