quick start

1. Dowload and unzip the windows, linux or mac version of fastsimcoal in the folder of your choice.
   
   The archives contain an executable version of fastsimcoal for a given platform, the fastsimcoal pdf manual, as well as examples par files and example template (tpl), distribution (est),  and definition files (def) for a veriety of simple evolutionary scenarios and several types of markers, with and without recombination.
   
   For the linux version, it may be necessary to make fastsimcoal executable. This is done by just typing
   
   chmod +x ./fastsimcoal2
   
   
   
2. Running fastsimcoal
   There are 3 ways to simulate genetic data with fastsimcoal
   
   
   1) Simulate data under an evolutionary scenario with parameter values defined in an input parameter file
   

   
   ./fastsimcoal2 -i test.par -n 100
   
   fastsimcoal2 will use the scenario and the parameter values defined in the parameter file test.par and make 100 simulations under this scenario.
   
   

   2) Simulate data under an evolutionary scenario with parameter values randomly drawn from priors
   

   
   ./fastsimcoal2 –t test.tpl –n 10 –e test.est –E 100
   
   fastsimcoal2 will use the scenario defined in the template file test.tpl and generate 100 sets of parameter values by randomly drawing these values from the priors defined in the file test.est. 10 simulations will be done for each sets of randomly drawn parameter values.
   
   

   3) Simulate data under an evolutionary scenario with parameter values defined in an external definition file
   

   
   ./fastsimcoal2 -t test.tpl -n 100 -f test.def
   
   fastsimcoal2 will use the scenario defined in the template file test.tpl and use the parameter values found in the definition file test.def. 100 simulations will be done for each set of predefined parameter values.
   

command line options

example files

Last updated by L. Excoffier on 15.02.2013