10 20 6 3 

1 1 0.75

m s m 

2 5 0 3 0 4 0 2 0 0 1

1 0 1000
1 0 1000
1 0 1000
1 0 1000
1 0 1000
1 0 1000

1 0 1000
1 0 1000
1 0 1000
1 0 1000
1 0 1000

3 100 50000

1 0 0.01
1 0 0.01
1 0 0.01
1 0 0.01
1 0 0.01
1 0 0.01

0
3 1 1
0
0


1 -3.18 0.05 0 0 
1 -4.18 0.05 0 0 

0 
0

0
----------------------------------------------------------------------------------------
PopABC - Mark Beaumont & Joao Lopes                                             01/05/09

>no_iterations, generation_time, no_populations, no_loci

>escalar per locus (autosome - 1; X-linked - 0.75;  Y-linked or mitDNA - 0.25)

>type of DNA data (s - sequence; m - microssatelites)

>topology:       2 - specify topology manually [e.g. ((Pop1,Pop2)Pop3) -> 1 2 2 3];
                 5 - specify topology manually (and choose a Model marker).       

>ne1 params:     1 - uniform distribtuion;
                 2 - generalized gamma distribution;
>ne2 params
>ne3 params
>ne4 params
>ne(...)

>neanc1 params
>neanc2 params
>neanc3 params
>(...) params

>t1 params:      1 - uniform distribtuion;
                 2 - generalized gamma distribution;
                 3 - uniform distribtuion (for all time events);
                 4 - generalized gamma distribution (for all time events);
                 [for 1 and 2 t(n) is added to t(n+1)]
                 [for 3 and 4 set only one priors for all t(n)] 
>t2 params
>t3 params
>(...) params

>mig1 params:    0 - no migration;
                 1 - uniform distribtuion;
                 2 - generalized gamma distribution;
                 3 - uniform distribtuion (on number of migrations);
                 4 - generalized gamma distribution (on number of migrations).
                 [for 3 and 4 real mig rate is calculated as nmig/Ne]
>mig2 params
>mig3 params
>mig4 params
>(...)

>miganc1 params
>miganc2 params
>(...)

>mutM params:    0 - zero mutation;
                 1 - lognormal distribution: (mean of mean(log10); stdev of mean(log10);
                 mean of Sdev(log10); stdev of stdev(log10). Stdev truncated at 0.
                 2 - normal distribution: (mean of mean; stdev of mean; mean of Sdev;
                 stdev of stdev. Stdev truncated at 0.
>mutS params

>recM params:    0 - zero recombination;
                 1 - lognormal distribution: (mean of mean(log10); stdev of mean(log10);
                 mean of Sdev(log10); stdev of stdev(log10). Stdev truncated at 0.
                 2 - normal distribution: (mean of mean; stdev of mean; mean of Sdev;
                 stdev of stdev. Stdev truncated at 0.

>recS params                 

>migweight:      0 - do not use migweights matrix;
                 1 - use migweights matrix as following:
                 
                 0     mw112 mw113 mw114 mw115 ...
                 0     mw122 mw123 mw124 mw125 ...
                 0     mw132 mw133 mw134 mw135 ...
                 0     mw142 mw143 mw144 mw145 ...
                 ...   ...   ...   ...   ...   ...
                 
                 mw211 0     mw213 mw214 mw215 ...
                 mw221 0     mw223 mw224 mw225 ...
                 mw231 0     mw233 mw234 mw235 ...
                 mw241 0     mw243 mw244 mw245 ...
                 ...   ...   ...   ...   ...   ...

                 mw311 mw312 0     mw314 mw315 ...
                 mw321 mw322 0     mw324 mw325 ...
                 mw331 mw332 0     mw334 mw335 ...
                 mw341 mw342 0     mw344 mw345 ...
                 ...   ...   ...   ...   ...   ...

                 mw411 mw412 mw413 0     mw415 ...
                 mw421 mw422 mw423 0     mw425 ...
                 mw431 mw432 mw433 0     mw435 ...
                 mw441 mw442 mw443 0     mw445 ...
                 ...   ...   ...   ...   ...   ...
                 
                 mw511 mw512 mw513 mw514 0     ...
                 mw521 mw522 mw523 mw524 0     ...
                 mw531 mw532 mw533 mw534 0     ...
                 mw541 mw542 mw543 mw544 0     ...
                 ...   ...   ...   ...   ...   ...

                 ...
                 
                 , where mwitj is the prob that the fraction of migrantes in pop i comes
                 from pop j at a period of time before time event t. Sum of prob should
                 be equal to 1.        
                 [only use migweight if the topology is specified (option 1,2,4 or 5)]