Table 1 List of population genetic simulation software

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[28–30]

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

•

•