runs		diploid	constantMetapopSize
2		true		true



chromsize	numcroms	popsizeKmax	Numpops	maxgen 	mutRate per haploid genome	Rec
1000		1		1000		1		200		1					0.0


recurrentmut retromut 
true	true		

# this defines a MG94 codon evolution model with dN/dS = 0.5
codon omega
true	0.5

#default sample size is 20, to change it:
sample size
50			


# allowed model of nuc substit: GTR (Tavare 1982; Zarkihk 1994), SYM (Zarkihk 1994), JC (4 alleles)

model
GTR

#rates are AC AG AT CG CT GT
rates
3.0 5.0 0.9 1.3 5.3 1.0

# the first there equilibrium freqs: A C G
freqs
0.35 0.17 0.23