popsimulate: A C repository from pbeerli

To generate simulated datasets do this:
[check out the example directory]
migtree < parmfile.sequence | migdata 

it will print some auxillary stuff to the screen but will 
produce a file called infile with the sequences in it.

migdata is not interactive and gets all its stuff through the migtree
output what that is you can check by doing
migtree < parmfile.stepstone > trees
and then look at trees

Here an example parmfile for the simulator
I explain each line after #
the parmfile for the simulator cannot contain any comment!

#for sequences	
S Nogamma 1.0      # {S: datatype [S, A, M = seq, allelic, microsat]} 
                   # {Nogamma:  site mutation rate is NOT gamma deviated}
                   # { if you want to use Gamma let me know [->more explan}
		   # the 1.0 is for future development, 1.0=coalescent
4 3 9839017        # number_of_populations number_of_loci random_number_seed
                   # the random number seed should be of the type 4n+1
 10 10 10 10       # sample size for each population
100 100 100 100    # population size for each population, remember this
                   # this gets multiplied by and 4 -> theta=4 N mu
- 0 0 0            # immigration matrix - on diagonal 
0.00125 - 0 0      # this example has no migration except from
0 0.00125 - 0      #  1->2->3->4
0 0 0.00125 -      #
0.0000125          # mutation rate per site
1000 2.0           # number_of_sites t/t_ratio

#for  microsatellites
M Nogamma 1.0      # {S: datatype [S, A, M = seq, allelic, microsat]} 
                   # {Nogamma:  site mutation rate is NOT gamma deviated}
                   # { if you want to use Gamma let me know [->more explan}
		   # the 1.0 is for future development: 1.0 = coalescent
4 3 983 901 7      # number_of_populations number_of_loci random_number_seed1 2 3
                   # the random number seed should be of the type 4n+1
 10 10 10 10       # sample size for each population
100 100 100 100    # population size for each population, remember this
                   # this gets multiplied by and 4 -> theta=4 N mu
- 0 0 0            # immigration matrix - on diagonal 
0.00125 - 0 0      # this example has no migration except from
0 0.00125 - 0      #  1->2->3->4
0 0 0.00125 -      #
0.00125            # mutation rate per site
1000               # number_of_sites
pbeerli/popsimulate
