Compilation and Running

Compilation and running

Compiling the code

The code can be compiled simply with the command g++ -O3 *.cc. This will create a.out executable. A Makefile is included; simply typing make creates executable FS.

To run with default parameters, simply type ./FS in the current working directory. The default parameters correspond to one population of 10,000 individuals evolving for 4 x 2N = 80,000 generations with mutation rate µ = 10^-8, recombination rate r = 10^-8, under no selection (random drift). This is a default burnin period. The run time is about 30 minutes on an 1.8GHz processor.

The output will contain log file with the parameters of the simulation, vcf file for Population 1, and the allele frequency distribution file for Population 1.

Output

The output file names are specified by command line argument -o followed by file name root. For example, ./FS -o fs1 will create the following files in the working directory:

fs1.log
fs1.sequences.population1.burnin.vcf
fs1.derivedAlleleFrequency.population1.burnin
...
fs1.sequences.population1.final.vcf
fs1.derivedAlleleFrequency.population1.final