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Table 1 List of population genetic simulation software

From: A survey of genetic simulation software for population and epidemiological studies

Name, description and URL Lang. Loc. R? S? ~N? G? D?
Backwards simulators        
CoaSim[2]
Requires additional user coding for more complex models.
http://www.daimi.au.dk/~mailund/CoaSim/
Scheme or Python s,c   
COSI[3]
Allows variable recombination.
http://www.broad.mit.edu/~sfs/cosi
C s,c     
FastCoal[4]
Variable recombination and mutation models require additional post-processing.
http://chp220mac.hsc.usc.edu/Marjoram/Software.html
C + + s,c   
GeneArtisan[5]
Flexible disease models. Selection allowed.
http://www.rannala.org/
C + + s,c  
GENOME[6]
Infinite sites discrete-generation model.
http://www.sph.umich.edu/csg/liang/genome/
C + + s   
mlcoalsim[7]
Flexible extensions to ms program.
http://www.ub.es/softevol/mlcoalsim
C s,c   
ms[8]
Efficient, well-used program. Can pipe into SeqGen for additional mutation models.
http://home.uchicago.edu/~rhudsonl/source/mksamples.html
C s,c     
msHOT[9]
Allows variable recombination. Can pipe to SeqGen.
http://home.uchicago.edu/~rhudsonl/source/mksamples.html
C s,c     
newgenecoal[10]
Specialist software for gene duplications and large CNVs.
http://molpopgen.org/software/coalescent.html
C s,c     
Recodon[11]
Designed for exons -- allows codon-specific mutation model.
http://darwin.uvigo.es/
C s    
SARG[12]
Flexible. Mathematica front-end.
http://walnut.usc.edu/Members/magnus/software/software/
C + + s   
SeiSlm[13]
Selected site must be diallelic, but various mutational models allowed for other sites.
http://mathgen.stats.ox.ac.uk/software.html
C + + s,c    
Serial SimCoal [14]
Allows sampling from different time points.
http://iod.ucsd.edu/simplex/ssc/
C + + s,c     
SIMCOAL[15]
Discrete-generation model. Flexible demographic options.
http://cmpg.unibe.ch/software/simcoal/
C + + s,c     
SIMCOAL[16]
Allows variable recombination and > 1 coalescence per generation.
http://cmpg.unibe.ch/software/simcoal2/
C + + s,c    
SNPsim[17]
Infinite sites model.
http://darwin.uvigo.es/software/snpsim.html
c s    
SPLATCHE[18]
Complex demographies via 2D demic isolation-by-distance model.
http://cmpg.unibe.ch/software/splatche/
C + + s,c     
TREEVOLVE[19]
Finite sites model.
http://evolve.zoo.ox.ac.uk/software.html?name=Treevolve
C s    
Forward simulators        
BottleSim[20]
Simulates population bottlenecks. No mutational models.
http://chkuo.name/software/BottleSim.html
C + + -     
EasyPOP[21]
Allows complex demographies.
http://www.unil.ch/dee/page36926_fr.html
C s,c    
FORWSIM[22]
Efficient 'look-ahead' procedure, but limited model options.
http://www.people.cornell.edu/pages/bp85/
C + + s     
FPG
Infinite sites model.
http://lifesci.rutgers.edu/~heylab/heylabsoftware.htm
C s    
FREGENE[23]
Diallelic loci only, finite sites allowed. Rescaling option adds computational efficiency.
www.ebi.ac.uk/projects/BARGEN
C + + s
GenomePop[24]
Flexible but no ascertained sampling. Rescaling option adds computational efficiency.
http://webs.uvigo.es/acraaj/GenomePop.htm
C + + s  
GenomeSIM[25]
Genome-wide data only possible if small N generations simulated.
http://chgr.mc.vanderbilt.edu/genomeSIMLA/genomeSIMLA/lntroduction.html
C + + s   
Mendel's Accountant[26]
Flexible mutation and selection options.
http://mendelsaccountant.info/
C + + s  
Nemo[27]
Flexible demographic options, requires user coding.
http://nemo2.sourceforge.net/
C + + s,c  
SFS_CODE
Finite sites model.
http://cbsuapps.tc.cornell.edu/sfscode.aspx or http://sfscode.sourceforge.net/
C s   
simuPOP[2830]
Requires additional user coding for more complex models.
http://simupop.sourceforge.net/
Python s,c  
Sideways simulators        
gs[31]
Stochastic haplotype extension method. Two-locus unlinked disease model.
http://vorlon.case.edu/~jxl175/gs.html
C + + s   na na
GWAsimulator[32]
Stochastic haplotype extension method. Multi-locus unlinked disease model.
http://biostat.mc.vanderbilt.edu/GWAsimulator
C + + s   na na
hapgen[33]
Coalescent-with-recombination approximation generates 'missing data'.
http://www.stats.ox.ac.uk/~marchini/software/gwas/hapgen.html
C s    
HAP-SAMPLE[34]
Bootstrap resampling from HapMap plus a single generation of recombination.
http://www.hapsample.org/
Web-based s na na
  1. Key:
  2. Lang. Programming language
  3. Loc. Locus types allowed. s = SNPs, c = CNVs (including microsatellites)
  4. R? Recombination allowed?
  5. S? Selection allowed?
  6. ~N? Variable population size and/or population structure allowed?
  7. G? Genome-wide data possible?
  8. D? Disease model allowed? (for ascertained samples such as case-control)
  9. na Not applicable
  10. CNV Copy number variation