Fast sequential Markov coalescent simulation of genomic data. fastsimcoal help you efficiently generate genetic diversity for different types of markers along large genomic regions, for both present or ancient samples. It includes a parameter sampler allowing its integration into Bayesian or likelihood parameter estimation procedure.

Usage:
-h --help : prints this help
-i --ifile test.par : name of parameter file
-n --numsims 1000 : number of simulations to perform
-t --tfile test.tpl : name of template parameter file (optional)
-f --dfile test.def : name of parameter definition file (optional)
-F --dFile test.def : same as -f, but only uses simple parameters defined in template file. Complex params are recomputed
-e --efile test.est : parameter prior definition file (optional) Parameters drawn from specified distributions are substituted into template file.
-E --numest 10 : number of estimations from parameter priors (optional) Listed parameter values are substituted in template file.
-g --genotypic : generates arlequin projects with genotypic data
-p --phased : specifies that phase is known in arlequin output default: phase is unknown
-s --dnatosnp : output DNA as SNP data (0: ancestral or 1: derived)
-I --inf : generates DNA mutations according to an infinite site (IS) mutation model
-d --dsfs : computes derived site frequency spectrum (for SNP data only).
-m --msfs : computes minor site frequency spectrum (for SNP data only)
-H --header : generates header in site frequency spectrum files.
-q --quiet : minimal message output to console
-T --tree : output coalescent tree in nexus format
-k --keep 10000 : number of simulated polymorphic sites kept in memory If the simulated no. is larger, then temporary files are created

fastsimcoal can handle very complex evolutionary scenarios including an arbitrary migration matrix between samples, historical events allowing for population resize, population fusion and fission, admixture events, changes in migration matrix, or changes in population growth rates. The time of sampling can be specified independently for each sample, allowing for serial sampling in the same or in different populations.

The license of this software is Freeware, you can free download and free use this calculator software.