# Two populations with 10 independent SNPs fixed for different alleles each.
# NOTE that the initially given population size are overwritten to be distinct and of size 100 and 120


Biological Model
viral

chromsize	numcroms	popsizeKmax	Numpops	maxgen 	HaploidGenomemutRate		Rec
10		1		1000		2	200		0.000001	0

independentsnps
true

# the next line is unnecessary, with 2 pops island = 1dim-stepping stone (default model)

flowmodel
ISLAND

migration
0.01

recurrentmut
true true

runs		diploid	constantMetapopSize
1		true		false

# the following line overwrites the popsizeKmax value for each population
# if, for example we change the pop2 size to be 12000 we will see the invasion of allele 2 in the pop 1

different pop sizes
100 120

sample size 
20


model
jc2

# next line fixes pop 1 with all 1's and pop2 with all 2's

SNP freqs
1.0 0.0