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seqfile = mtCDNApri.nuc
treefile = mtCDNApri.trees
outfile = mlc * main result file name
noisy = 3 * 0,1,2,3,9: how much rubbish on the screen
verbose = 1 * 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
clock = 0
aaDist = 7 * 0:equal, +:geometric; -:linear, 1-6:G1974,Miyata,c,p,v,a
aaRatefile = wag.dat * only used for aa seqs with model=empirical(_F)
* dayhoff.dat, jones.dat, wag.dat, mtmam.dat, or your own
model = 0
* 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, 7:AAClasses, 8:REVaa_0, 9:REVaa(nr=189)
NSsites = 0
icode = 1 * 0:universal code; 1:mammalian mt; 2-10:see below
fix_kappa = 0
kappa = 5
fix_omega = 0
omega = 0.2
getSE = 0
RateAncestor = 0
Small_Diff = .5e-6
cleandata = 1 * remove sites with ambiguity data (1:yes, 0:no)?
method = 0 * 0: simultaneous; 1: one branch at a time
fix_blength = 0 * 0: ignore, -1: random, 1: initial, 2: fixed, 3: proportional
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