SNPsim specifications


Unique identifier OMICS_15249
Name SNPsim
Software type Package/Module
Interface Command line interface
Restrictions to use None
Output data A file with diploid SNP genotypes that includes a header with the date and time of the simulation, the value of the parameters in command line style, the number of samples and individuals per sample, and the length of the region simulated.
Operating system Unix/Linux, Mac OS, Windows
Programming languages C
License GNU General Public License version 3.0
Computer skills Advanced
Version 0.8
Stability Stable
Maintained Yes




No version available

Publication for SNPsim

SNPsim citations


Computer Programs and Methodologies for the Simulation of DNA Sequence Data with Recombination

Front Genet
PMCID: 3561691
PMID: 23378848
DOI: 10.3389/fgene.2013.00009

[…] c genome-wide data (see, Arbiza et al., ).Again, an alternative methodology consists of the use of two simulators. A few programs currently implement the simulation of recombination hotspots, namely, SNPsim (Wiuf and Posada, ), cosi (Schaffner et al., ), GENOME (Liang et al., ), mbs (Teshima and Innan, ), and msHOT (Hellenthal and Stephens, ). Although all these programs simulate particular geneti […]


A survey of genetic simulation software for population and epidemiological studies

Hum Genomics
PMCID: 3525177
PMID: 19129092
DOI: 10.1186/1479-7364-3-1-79

[…] of simulating just that part of the genealogy needed to produce the data in the simulated sample. Richard Hudson's ms program []remains one of the most popular for straightforward problems. msHOT, [] SNPsim [] and COSI [] extend the algorithm to allow variable recombination rates along the DNA sequence, and msHOT, COSI, CoaSim [] and newgenecoal [] also allow (allelic) gene conversion in addition […]

SNPsim institution(s)
Variagenics Inc, Cambridge, MA, USA

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