5 Additional command line options

Table 4: Summary of FREGENE command line options. Further details are given in the text.

Option USAGE		Description
-i file_name		Specifies the input file (required)
-p file_name		Specifies the parameter file (required)
-recomb file_name		Specifies the recombination model (required)
-o file_name		Specifies the output file (required)
-SELECT void		Enables selection
-SELFING float		Enables self reproduction with specified selfing fraction
-mg void		Enables migration between subpopulations
-gn int		Specifies the number of generations
-sub int...int		Describes the population structure: number and sizes of subpopulations
-subout int...int		Modifies the subpopulation sizes (but not the number of subpopulations)
-os int...int		Defines the number of sequences output in each subpopulation
-r float		Specifies the population growth rate, $r$ (default 0 corresponds to no growth). If $r\ne0$ , in each generation the (real-valued) population size (individuals) is multiplied by $1{+}r$ then (temporarily) rounded up to an integer
-sd int		Specifies the random seed
-scale float		Enables scaling and specifies the scaling factor $\lambda$
-scale_exp float int		Like -scale float but adds extra generations (2nd argument) during which the population expands linearly to reach the target population size (specified by $<SEGMENTS>$ ).
-sel file_name		Location for list of selected sites gone to fixation
-hz file_name		Location for output of homozygozity over generations
-freq file_name		Location for counts of all minor alleles (selected or not) in final generation
-ADDS file_1...file_6		Locations for 6 tables used for detailed monitoring of simulation.
-af file_name		Location for description of polymorphic sites in final generation
-bckMut file_name		Location for list of back mutations
-dbleHit file_name		Location for list of double hits
-histAF int file_name		Specifies how often and where to save distribution of allele frequencies
-RecOut file_name		Location for positions and intensities of hotspots
-sel_LE int		Specifies the average # generations selected sites remain under selection if neither fixed nor lost.

• -SELECT option:
  This option does not require any argument. It is used to enable selection in the model. If not used, some selection-specific steps of the algorithm are avoided and FREGENE runs quicker.
• -SELFING float option:
  If chosen, self-reproduction is enabled. One parent is sampled at random, and then the second parent is the same as the first with the probability specified, and is otherwise chosen at random among individuals other than the first parent.

• -mg option:
  This option has no argument and, if chosen, enables migration between subpopulations, according to the backward migration matrix ($.i.e.$ the transpose of the migration matrix) defined in the parameter file.
• -gn int option:
  This option specifies the number of generations for the simulation run. If this option is chosen, the number of generations in the parameter file will be ignored.
• -sub int int ... int option:
  This option specifies the subpopulation structure of the starting population. Its first argument is the number of subpopulations ($K$ ). Then follows $K$ arguments corresponding the initial population sizes (numbers of chromosomes) of each subpopulation. If subpopulation sizes are not consistent with the ones in the input file ($e.g.$ in the case of successive runs), the run will terminate.

• -subout int int ... int option:
  This option allows the user to specify different sub-population sizes for the present run from those specified in the input file, arising from a previous run of FREGENE. The population expands (or contracts) in the first generation to the desired sizes. The number of subpopulations (first argument) must be equal to the one in the input file (or the one defined in the -sub option), otherwise FREGENE stops.
• -os int int ... int option:
  This option specifies the number of sequences (scaled) at output in each subpopulation. As for -subout option, the first argument (the number of subpopulations) must be consistent with the input file and/or -sub option. Furthermore, the number of sequences in each subpopulation must be lower or equal to the number of sequences simulated, otherwise, the run is stopped.
• -r float option:
  The population growth rate for subdivided populations ($i.e.$ -sub option must also be assigned). It can also be set in the parameter file (see Table 2). Default value is 0 , corresponding to a constant size population.
• -sd option:
  Specifies the random seed used. FREGENE automatically changes the seed between two successive runs, but setting the seed can allow replicate runs.
• -scale float option:
  This option enables the scaling of the population and its argument defines the scaling factor ($\lambda$ ). Scaling reduces by a factor $\lambda$ both the population size and the number of generations, and increases similarly the overall recombination rate, the mutation rate and the selection coefficient $s$ . The use of scaling results in a large drop in computation time and memory requirement at the cost of some approximation; in particular scaling increases the rate of double-hit and back mutations. The final population size will be $\lambda$ times smaller than specified by $<SEGMENTS>$ in the input file.

• -scale_exp float int option:
  This option also enables the scaling of the simulation, but still outputs the number of chromosomes specified by $<SEGMENTS>$ . A number of generations (2nd argument), is added to the simulation, during which the population expands linearly (the population size in each generation rounded up to an even integer).
• -sel_LE int option:
  The mean number of generations before selection is ``switched off'' at a selected site (default 75,000). The inverse of this number is the probability per generation that selection is switched off (so selection operates at each selected site for a time that is random with the geometric distribution, mean LE).