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.

Imperial College -- August 2008