SIB fastsimcoal University of Berne

fast sequential Markov coalescent simulation of genomic data under complex evolutionary models

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 ./fastsimcoal


  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

    ./fastsimcoal -i test.par -n 100

    fastsimcoal 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

    ./fastsimcoal –t test.tpl –n 10 –e test.est –E 100

    fastsimcoal     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

    ./fastsimcoal -t test.tpl -n 100 -f test.def

    fastsimcoal 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

fastsimcoal can be launched in many different ways with several options. Supported command line options can be seen by typing

            fastsimcoal -h

which would produce an output looking like

fastsimcoal help screen

Additional information on command-line options are found in the  manual.

example files

All example files mentioned in fastsimcoal manual can be found in the subdirectory "example files" where you installed fastsimcoal. They include the following par files

1PopDNA.par
1PopDNArec.par
1PopDNAserial.par
1PopMultiLocus.par
1PopMultiLocusDiffChrom.par
2PopDNArec.par
2popSTRdiv.par
2popSTRmigr.par
3PopDNASFS.par

These files can be immediately used by fastsimcoal, once you have copied fastsimcoal in the same directory as the par file, and that ou have opened a console window in this directory.

For instance, typing

./fastsimcoal -i 1PopDNA.par -n 10

will launch 10 simulations of the scenario defined in the the parameter file 1PopDNA.par
back to fastsimcoal home page

Last updated by L. Excoffier on 21.02.2011
 Document made with KompoZer