cosi2 is an efficient coalescent simulator with support for selection, population structure, variable recombination rates, and gene conversion. It supports exact and approximate simulation modes.
Two working examples are included in the examples/ subdirectory, and documentation is in the documentation/ directory.
Conditional defines that affect cosi compilation:
Defines that affect behavior:
COSI_RECOMB_CONSTRATE - if defined, optimizes cosi to support only constant recombination rate. By default, cosi supports variation of recombination rate across the region.
COSI_GC_DISABLE - if defined, disables support for gene conversion.
Defines that affect only CPU and memory requirements, but not the output:
COSI_IMPL_STORE_GLOC_IN_LOC - if defined, genetic map locations are stored with each physical location. This allows constant-time mapping between the two, at the cost of extra memory usage; is useful when the region is large and the recombination rate changes at many points in the region.
COSI_SLOWRECOMB - use the slower method of choosing recomb rates