GSR: Simulator - SFS_CODE

Basic Package Attributes
AttributeValue
Title SFS_CODE
Short Description SFS_CODE can perform forward population genetic simulations under a general Wright-Fisher model with arbitrary migration, demographic, selective, and mutational effects.
Long Description SFS_CODE (Selection on Finite Sites under COmplex Demographic Events) performs forward population genetic simulations under a general Wright-Fisher model with arbitrary demographic, selective, and mutational effects.
Version 20100203
Project Started 2009
Last Release 8 years, 6 months ago
Homepagehttp://sfscode.sourceforge.net/SFS_CODE/index/index.html
Citations Hernandez RD, A flexible forward simulator for populations subject to selection and demography., Bioinformatics, 12-01-2008 [ Abstract, cited in PMC ]
GSR CertificationGSR-certified

Accessibility
Documentation
Application
Support

Last evaluated10-15-2015 (1829 days ago)
Detailed Attributes
Attribute CategoryAttribute
Target
Type of Simulated DataDiploid DNA Sequence, Haploid DNA Sequence, Sex Chromosomes,
VariationsBiallelic Marker, Multiallelic Marker, Single Nucleotide Variation, Insertion and Deletion, Other (Large-scale insertions and deletions),
Simulation MethodForward-time, Other (Rejection sampling to simulate data conditional on terminal frequency.),
Input
Data TypeAllele Frequencies, Other (Recombination rate variation),
File formatMS, STRUCTURE, Program Specific, Other (Fasta),
Output
Data TypeGenotype or Sequence, Demographic, Mutation, Diversity Measures, Fitness,
Sequencing ReadsOther (Coding or noncoding, sex/autosomal),
File FormatFasta or Fastq, MS, STRUCTURE, Program Specific, Other (Various),
Sample TypeRandom or Independent,
Phenotype
Trait Type
Determinants
Evolutionary Features
Demographic
Population Size ChangesConstant Size, Exponential Growth or Decline, Logistic Growth, Bottleneck, Carrying Capacity, User Defined,
Gene FlowStepping Stone Models, Island Models, Continent-Island Models, Sex or Age-Specific Migration Rates, Admixed Population, User-defined Matrix, Other (Various),
Spatiality
Life CycleDiscrete Generation Model, User-Defined transition matrices,
Mating SystemRandom Mating, Polygamous, Haplodiploid, Selfing, Other (Arbitrary poidy),
FecundityConstant Number, Individually Determined,
Natural Selection
DeterminantSingle-locus, Multi-locus, Codon-based, Fitness of Offspring,
ModelsDirectional Selection, Balancing Selection, Multi-locus models, Random Fitness Effects, Phenotype Threshold, Other (Various),
RecombinationUniform, Varying Recombination Rates, Gene Conversion Allowed,
Mutation ModelsTwo-allele Mutation Model, Markov DNA Evolution Models, Infinite-allele Model, Codon and Amino Acid Models, Indels and Others, Heterogeneity among Sites, Others,
Events AllowedPopulation Merge and Split, Varying Demographic Features, Population Events, Varying Genetic Features, Change of Mating Systems, Other (Various),
Other
InterfaceCommand-line, Script-based, Web-based,
Development
Tested PlatformsWindows, Mac OS X, Linux and Unix, Solaris, Others,
LanguageC or C++,
LicenseGNU Public License, BSD,
GSR CertificationAccessibility, Documentation, Application, Support,

The following 10 publications are selected examples of applications that used SFS_CODE.

2016

Subramanian S, The effects of sample size on population genomic analyses--implications for the tests of neutrality., BMC Genomics, 02-20-2016 [Abstract]

Lapierre M, Blin C, Lambert A, Achaz G, Rocha EP, The Impact of Selection, Gene Conversion, and Biased Sampling on the Assessment of Microbial Demography., Mol Biol Evol, 07-01-2016 [Abstract]

Kang L, Zheng HX, Zhang M, Yan S, Li L, Liu L, Liu K, Hu K, Chen F, Ma L, Qin Z, et al., MtDNA analysis reveals enriched pathogenic mutations in Tibetan highlanders., Sci Rep, 08-08-2016 [Abstract]

2015

Zhang Q, Tyler-Smith C, Long Q, An extended Tajima's D neutrality test incorporating SNP calling and imputation uncertainties., Stat Interface, 10-01-2015 [Abstract]

2014

He Z, O'Roak BJ, Smith JD, Wang G, Hooker S, Santos-Cortez RL, Li B, Kan M, Krumm N, Nickerson DA, Shendure J, et al., Rare-variant extensions of the transmission disequilibrium test: application to autism exome sequence data., Am J Hum Genet, 01-02-2014 [Abstract]

Wilson Sayres MA, Lohmueller KE, Nielsen R, Natural selection reduced diversity on human y chromosomes., PLoS Genet, 01-01-2014 [Abstract]

Simkin AT, Bailey JA, Gao FB, Jensen JD, Inferring the evolutionary history of primate microRNA binding sites: overcoming motif counting biases., Mol Biol Evol, 07-01-2014 [Abstract]

Sjöstrand AE, Sjödin P, Jakobsson M, Private haplotypes can reveal local adaptation., BMC Genet, 05-22-2014 [Abstract]

Fu W, Gittelman RM, Bamshad MJ, Akey JM, Characteristics of neutral and deleterious protein-coding variation among individuals and populations., Am J Hum Genet, 10-02-2014 [Abstract]

2013

Crisci JL, Poh YP, Mahajan S, Jensen JD, The impact of equilibrium assumptions on tests of selection., Front Genet, 01-01-2013 [Abstract]


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