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GSR: Simulator - SLiM
| Attribute | Value |
|---|---|
| Title | SLiM |
| Short Description | A framework for implementing forward genetic simulations, including an interactive development environment and a highly flexible scripting language. |
| Long Description | SLiM is an evolutionary simulation framework that combines a powerful engine for population genetic simulations with the capability of modeling arbitrarily complex eco-evolutionary scenarios. Simulations are configured via the integrated Eidos scripting language that allows interactive control over practically every aspect of the simulated scenarios. The underlying individual-based simulation engine is highly optimized to enable modeling of entire chromosomes in large populations. For macOS, Linux, and Windows (native and WSL) users, we also provide a graphical user interface for easy simulation set-up, interactive runtime control, and dynamical visualization of simulation output. |
| Keywords | population genetic simulator, forward-time, multiple species, coevolutionary dynamics |
| Version | 4.2.1 |
| Project Started | 2013 |
| Last Release | 1 week, 6 days ago |
| Homepage | https://messerlab.org/slim/ |
| Citations |
|
| GSR Certification |  ✔ Accessibility |
| Last evaluated | 09-07-2016 (2775 days ago) |
| Attribute Category | Attribute |
|---|---|
| Target | |
| Type of Simulated Data | Genotype at Genetic Markers, Diploid DNA Sequence, Haploid DNA Sequence, Sex Chromosomes, Mitochondrial DNA, Protein Sequence, Phenotype, |
| Variations | Biallelic Marker, Multiallelic Marker, Single Nucleotide Variation, Amino acid variation, Microsatellite, Insertion and Deletion, CNV, Inversion and Rearrangement, Alternative Splicing, Missing Genotypes, Genotype or Sequencing Error, Other, |
| Simulation Method | Forward-time, |
| Input | |
| Data Type | Allele Frequencies, Empirical, Ancestral Sequence, Saved simulation, Reference genome, Other, |
| File format | MS, Tree Sequence, Program Specific, Other, |
| Output | |
| Data Type | Genotype or Sequence, Phenotypic Trait, Individual Relationship, Demographic, Mutation, Linkage Disequilibrium, Diversity Measures, Fitness, |
| Sequencing Reads | Other, |
| File Format | Fasta or Fastq, MS, VCF, Tree Sequence, Program Specific, Other, |
| Sample Type | Random or Independent, Sibpairs, Trios and Nuclear Families, Extended or Complete Pedigrees, Case-control, Longitudinal, Other, |
| Phenotype | |
| Trait Type | Binary or Qualitative, Quantitative, Multiple, |
| Determinants | Single Genetic Marker, Multiple Genetic Markers, Sex-linked, Gene-Gene Interaction, Environmental Factors, Gene-Environment Interaction, |
| Evolutionary Features | |
| Demographic | |
| Population Size Changes | Constant Size, Exponential Growth or Decline, Logistic Growth, Bottleneck, Carrying Capacity, User Defined, |
| Gene Flow | Stepping Stone Models, Island Models, Continent-Island Models, Sex or Age-Specific Migration Rates, Influenced by Environmental Factors, Admixed Population, User-defined Matrix, Other, |
| Spatiality | Discrete Models, Continuous Models, Landscape Factors, |
| Life Cycle | Discrete Generation Model, Age structured, Overlapping Generation, User-Defined transition matrices, |
| Mating System | Random Mating, Monogamous, Polygamous, Haplodiploid, Selfing, Age- or Stage-Specific, Assortative or Disassortative, Other, |
| Fecundity | Constant Number, Randomly Distributed, Individually Determined, Influenced by Environment, Other, |
| Natural Selection | |
| Determinant | Single-locus, Multi-locus, Codon-based, Fitness of Offspring, Phenotypic Trait, Environmental Factors, |
| Models | Directional Selection, Balancing Selection, Multi-locus models, Epistasis, Random Fitness Effects, Disruptive, Phenotype Threshold, Frequency-Dependent, Other, |
| Recombination | Uniform, Varying Recombination Rates, Gene Conversion Allowed, |
| Mutation Models | Two-allele Mutation Model, Markov DNA Evolution Models, k-Allele Model, Infinite-allele Model, Infinite-sites Model, Stepwise Mutation Model, Codon and Amino Acid Models, Indels and Others, Heterogeneity among Sites, Others, |
| Events Allowed | Population Merge and Split, Varying Demographic Features, Population Events, Varying Genetic Features, Change of Mating Systems, Other, |
| Other | Phenogenetic, Polygenic background, |
| Interface | Command-line, Graphical User Interface, Integrated Development Environment, Script-based, |
| Development | |
| Tested Platforms | Windows, Mac OS X, Linux and Unix, |
| Language | C or C++, Other, |
| License | GNU Public License, |
| GSR Certification | Accessibility, Documentation, Application, Support, |
Number of Primary Citations: 5
Number of Non-Primary Citations: 87
The following 87 publications are selected examples of applications that used SLiM.
2018
Refoyo-Martínez, A., da Fonseca, R.R., Halldórsdóttir, K., Árnason, E., Mailund, T., & Racimo, F., Identifying loci under positive selection in complex population histories, bioRxiv, 10-25-2018 [Abstract]
Petr, M., Pääbo, S., Kelso, J., & Vernot, B., The limits of long-term selection against Neandertal introgression, bioRxiv, 07-04-2018 [Abstract]
Robinson, J.A., Brown, C., Kim, B.Y., Lohmueller, K.E., & Wayne, R.K., Purging of Strongly Deleterious Mutations Explains Long-Term Persistence and Absence of Inbreeding Depression in Island Foxes, Current Biology, 10-25-2018 [Abstract]
Lange, J.D., & Pool, J.E., Impacts of recurrent hitchhiking on divergence and demographic inference in Drosophila, bioRxiv, 07-11-2018 [Abstract]
Harris, A.M., & DeGiorgio, M., Identifying and classifying shared selective sweeps from multilocus data, bioRxiv, 10-17-2018 [Abstract]
de Koning, A.J., & De Sanctis, B.D., The Rate of Observable Molecular Evolution When Mutation May Not Be Weak, bioRxiv, 08-28-2018 [Abstract]
Kiwoong, N.A.M., Nhim, S., Robin, S., Bretaudeau, A., & Negre, N., Genomic differentiation is initiated without physical linkage among targets of divergent selection in Fall armyworms, bioRxiv, 10-25-2018 [Abstract]
Champer, J., Zhao, J., Champer, S., Liu, J., Messer, P.W., Population dynamics of underdominance gene drive systems in continuous space, bioRxiv, 10-22-2018 [Abstract]
Cheng, X., & DeGiorgio, M., Detection of shared balancing selection in the absence of trans-species polymorphism, bioRxiv, 09-22-2018 [Abstract]
Gazal, S., Loh, P.R., Finucane, H., Ganna, A., Schoech, A., Sunyaev, S., & Price, A., Low-frequency variant functional architectures reveal strength of negative selection across coding and non-coding annotations, bioRxiv, 04-09-2018 [Abstract]
Harris, R., Sackman, A., & Jensen, J.D., On the unfounded enthusiasm for soft selective sweeps II: examining recent evidence from humans, flies, and viruses, bioRxiv, 10-19-2018 [Abstract]
Hämälä, T., & Savolainen, O., Local adaptation under gene flow: Recombination, conditional neutrality and genetic trade-offs shape genomic patterns in Arabidopsis lyrata, bioRxiv, 07-23-2018 [Abstract]
Li, H., & Ralph, P., Local PCA shows how the effect of population structure differs along the genome, bioRxiv, 09-19-2018 [Abstract]
Mooney, J., Huber, C., Sul, J.H., Marsden, C., Zhang, Z., Sabatti, C., Ruiz-Linares, A., Bedoy, G., Costa Rica/Colombia Consortium for Genetic Investigation of Bipolar Endophenotypes, Freimer, N., & Lohmueller, K. E., Understanding the Hidden Complexity of Latin American Population Isolates, bioRxiv, 06-06-2018 [Abstract]
Parada, J.L.C., & Charlesworth, B., The effects on neutral variability of recurrent selective sweeps and background selection, bioRxiv, 06-29-2018 [Abstract]
Rougemont, Q., Carrier, A., Leluyer, J., Ferchaud, A.-L., Farrell, J., Hatin, D., Brodeur, P., & Bernatchez, L., Combining population genomics and forward simulations to investigate stocking impacts: A case study of Muskellunge (Esox masquinongy) from the St. Lawrence River basin, bioRxiv, 07-06-2018 [Abstract]
Kosheleva K, Desai MM, Recombination Alters the Dynamics of Adaptation on Standing Variation in Laboratory Yeast Populations., Mol Biol Evol, 01-01-2018 [Abstract]
Johnson KE, Voight BF, Patterns of shared signatures of recent positive selection across human populations., Nat Ecol Evol, 04-01-2018 [Abstract]
Sugden LA, Atkinson EG, Fischer AP, Rong S, Henn BM, Ramachandran S, Localization of adaptive variants in human genomes using averaged one-dependence estimation., Nat Commun, 02-19-2018 [Abstract]
Moon JM, Aronoff DM, Capra JA, Abbot P, Rokas A, Examination of Signatures of Recent Positive Selection on Genes Involved in Human Sialic Acid Biology., G3 (Bethesda), 03-28-2018 [Abstract]
Librado P, Orlando L, Detecting Signatures of Positive Selection along Defined Branches of a Population Tree Using LSD., Mol Biol Evol, 06-01-2018 [Abstract]
Zeng J, de Vlaming R, Wu Y, Robinson MR, Lloyd-Jones LR, Yengo L, Yap CX, Xue A, Sidorenko J, McRae AF, et al., Signatures of negative selection in the genetic architecture of human complex traits., Nat Genet, 05-01-2018 [Abstract]
Champer J, Liu J, Oh SY, Reeves R, Luthra A, Oakes N, Clark AG, Messer PW, Reducing resistance allele formation in CRISPR gene drive., Proc Natl Acad Sci U S A, 05-22-2018 [Abstract]
Rousselle M, Mollion M, Nabholz B, Bataillon T, Galtier N, Overestimation of the adaptive substitution rate in fluctuating populations., Biol Lett, 05-01-2018 [Abstract]
Guo J, Wu Y, Zhu Z, Zheng Z, Trzaskowski M, Zeng J, Robinson MR, Visscher PM, Yang J, Global genetic differentiation of complex traits shaped by natural selection in humans., Nat Commun, 05-14-2018 [Abstract]
Henden L, Lee S, Mueller I, Barry A, Bahlo M, Identity-by-descent analyses for measuring population dynamics and selection in recombining pathogens., PLoS Genet, 05-23-2018 [Abstract]
Patel R, Scheinfeldt LB, Sanderford MD, Lanham TR, Tamura K, Platt A, Glicksberg BS, Xu K, Dudley JT, Kumar S, Adaptive Landscape of Protein Variation in Human Exomes., Mol Biol Evol, 08-01-2018 [Abstract]
Tennessen JA, Gene buddies: linked balanced polymorphisms reinforce each other even in the absence of epistasis., PeerJ, 06-28-2018 [Abstract]
Fijarczyk A, Dudek K, Niedzicka M, Babik W, Balancing selection and introgression of newt immune-response genes., Proc Biol Sci, 08-15-2018 [Abstract]
Pouyet F, Aeschbacher S, Thiéry A, Excoffier L, Background selection and biased gene conversion affect more than 95% of the human genome and bias demographic inferences., Elife, 08-23-2018 [Abstract]
Sato DX, Kawata M, Positive and balancing selection on <i>SLC18A1</i> gene associated with psychiatric disorders and human-unique personality traits., Evol Lett, 08-21-2018 [Abstract]
Booker TR, Keightley PD, Understanding the factors that shape patterns of nucleotide diversity in the house mouse genome., Mol Biol Evol, 10-08-2018 [Abstract]
Harris AM, Garud NR, DeGiorgio M, Detection and Classification of Hard and Soft Sweeps from Unphased Genotypes by Multilocus Genotype Identity., Genetics, 10-12-2018 [Abstract]
Kim BY, Huber CD, Lohmueller KE, Deleterious variation shapes the genomic landscape of introgression., PLoS Genet, 10-22-2018 [Abstract]
2017
Peyregne, S., Boyle, M.J., Dannemann, M., & Prufer, K., Detecting ancient positive selection in humans using extended lineage sorting, bioRxiv, 04-19-2017 [Abstract]
Aeschbacher, S., Packard Selby, J., Willis, J.H., & Coop, G., Population-genomic inference of the strength and timing of selection against gene flow, bioRxiv, 06-07-2017 [Abstract]
Cahill, J.A., Heintzman, P.D., Harris, K., Teasdale, M., Kapp, J., Soares, A.E.R., Stirling, I., Bradley, D., Edwards, C.J., Kisleika, A.A., Malev, A.V., Monaghan, N., Green, R.E., Shapiro, B., Genomic evidence of globally widespread admixture from polar bears into brown bears during the last ice age, bioRxiv, 06-25-2017 [Abstract]
Schiffels, S., Mustonen, V., & Lässig, M., The asexual genome of Drosophila, bioRxiv, 11-29-2017 [Abstract]
Matz, M.V., Treml, E.A., Aglyamova, G.V., et al., Potential for rapid genetic adaptation to warming in a Great Barrier Reef coral, bioRxiv, 06-18-2017 [Abstract]
Laenen, B., Tedder, A., Nowak, M.D., et al., Demography and mating system shape the genome-wide impact of purifying selection in Arabis alpina, bioRxiv, 05-04-2017 [Abstract]
Racimo F, Marnetto D, Huerta-Sánchez E, Signatures of Archaic Adaptive Introgression in Present-Day Human Populations., Mol Biol Evol, 02-01-2017 [Abstract]
Pedersen CT, Lohmueller KE, Grarup N, Bjerregaard P, Hansen T, Siegismund HR, Moltke I, Albrechtsen A, The Effect of an Extreme and Prolonged Population Bottleneck on Patterns of Deleterious Variation: Insights from the Greenlandic Inuit., Genetics, 02-01-2017 [Abstract]
Racimo F, Gokhman D, Fumagalli M, Ko A, Hansen T, Moltke I, Albrechtsen A, Carmel L, Huerta-Sánchez E, Nielsen R, Archaic Adaptive Introgression in TBX15/WARS2., Mol Biol Evol, 03-01-2017 [Abstract]
Liu Q, Zhou Y, Morrell PL, Gaut BS, Deleterious Variants in Asian Rice and the Potential Cost of Domestication., Mol Biol Evol, 04-01-2017 [Abstract]
Kardos M, Qvarnström A, Ellegren H, Inferring Individual Inbreeding and Demographic History from Segments of Identity by Descent in <i>Ficedula</i> Flycatcher Genome Sequences., Genetics, 03-01-2017 [Abstract]
Nam K, Munch K, Mailund T, Nater A, Greminger MP, Krützen M, Marquès-Bonet T, Schierup MH, Evidence that the rate of strong selective sweeps increases with population size in the great apes., Proc Natl Acad Sci U S A, 02-14-2017 [Abstract]
Kim BY, Huber CD, Lohmueller KE, Inference of the Distribution of Selection Coefficients for New Nonsynonymous Mutations Using Large Samples., Genetics, 05-01-2017 [Abstract]
Rogers RL, Slatkin M, Excess of genomic defects in a woolly mammoth on Wrangel island., PLoS Genet, 03-02-2017 [Abstract]
Bay RA, Ruegg K, Genomic islands of divergence or opportunities for introgression?, Proc Biol Sci, 03-15-2017 [Abstract]
Haller BC, Messer PW, asymptoticMK: A Web-Based Tool for the Asymptotic McDonald-Kreitman Test., G3 (Bethesda), 05-05-2017 [Abstract]
Huber CD, Kim BY, Marsden CD, Lohmueller KE, Determining the factors driving selective effects of new nonsynonymous mutations., Proc Natl Acad Sci U S A, 04-25-2017 [Abstract]
Librado P, Gamba C, Gaunitz C, Der Sarkissian C, Pruvost M, Albrechtsen A, Fages A, Khan N, Schubert M, Jagannathan V, et al., Ancient genomic changes associated with domestication of the horse., Science, 04-28-2017 [Abstract]
Sohail M, Vakhrusheva OA, Sul JH, Pulit SL, Francioli LC, Genome of the Netherlands Consortium., Alzheimer’s Disease Neuroimaging Initiative., van den Berg LH, Veldink JH, de Bakker PIW, et al., Negative selection in humans and fruit flies involves synergistic epistasis., Science, 05-05-2017 [Abstract]
Booker TR, Ness RW, Keightley PD, The Recombination Landscape in Wild House Mice Inferred Using Population Genomic Data., Genetics, 09-01-2017 [Abstract]
Gazal S, Finucane HK, Furlotte NA, Loh PR, Palamara PF, Liu X, Schoech A, Bulik-Sullivan B, Neale BM, Gusev A, et al., Linkage disequilibrium-dependent architecture of human complex traits shows action of negative selection., Nat Genet, 10-01-2017 [Abstract]
Xu D, Pavlidis P, Taskent RO, Alachiotis N, Flanagan C, DeGiorgio M, Blekhman R, Ruhl S, Gokcumen O, Archaic Hominin Introgression in Africa Contributes to Functional Salivary MUC7 Genetic Variation., Mol Biol Evol, 10-01-2017 [Abstract]
Siewert KM, Voight BF, Detecting Long-Term Balancing Selection Using Allele Frequency Correlation., Mol Biol Evol, 11-01-2017 [Abstract]
Sikora M, Seguin-Orlando A, Sousa VC, Albrechtsen A, Korneliussen T, Ko A, Rasmussen S, Dupanloup I, Nigst PR, Bosch MD, et al., Ancient genomes show social and reproductive behavior of early Upper Paleolithic foragers., Science, 11-03-2017 [Abstract]
Eichstaedt CA, Pagani L, Antao T, Inchley CE, Cardona A, Mörseburg A, Clemente FJ, Sluckin TJ, Metspalu E, Mitt M, et al., Evidence of Early-Stage Selection on EPAS1 and GPR126 Genes in Andean High Altitude Populations., Sci Rep, 10-12-2017 [Abstract]
Morgan AP, Pardo-Manuel de Villena F, Sequence and Structural Diversity of Mouse Y Chromosomes., Mol Biol Evol, 12-01-2017 [Abstract]
Comeron JM, Background selection as null hypothesis in population genomics: insights and challenges from <i>Drosophila</i> studies., Philos Trans R Soc Lond B Biol Sci, 12-19-2017 [Abstract]
Cheng X, Xu C, DeGiorgio M, Fast and robust detection of ancestral selective sweeps., Mol Ecol, 12-01-2017 [Abstract]
Antelope CX, Marnetto D, Casey F, Huerta-Sanchez E, Leveraging Multiple Populations across Time Helps Define Accurate Models of Human Evolution: A Reanalysis of the Lactase Persistence Adaptation., Hum Biol, 01-01-2017 [Abstract]
2016
Cassa, C.A., Weghorn, D., Balick, D.J., et al., Estimating the selective effect of heterozygous protein truncating variants from human exome data, bioRxiv, 09-16-2016 [Abstract]
Ewing GB, Jensen JD, The consequences of not accounting for background selection in demographic inference., Mol Ecol, 01-01-2016 [Abstract]
Racimo F, Testing for Ancient Selection Using Cross-population Allele Frequency Differentiation., Genetics, 02-01-2016 [Abstract]
Galtier N, Adaptive Protein Evolution in Animals and the Effective Population Size Hypothesis., PLoS Genet, 01-01-2016 [Abstract]
de Filippo C, Key FM, Ghirotto S, Benazzo A, Meneu JR, Weihmann A, Parra G, Green ED, Andrés AM, Recent Selection Changes in Human Genes under Long-Term Balancing Selection., Mol Biol Evol, 06-01-2016 [Abstract]
Harris K, Nielsen R, The Genetic Cost of Neanderthal Introgression., Genetics, 06-01-2016 [Abstract]
Enard D, Cai L, Gwennap C, Petrov DA, Viruses are a dominant driver of protein adaptation in mammals., Elife, 05-17-2016 [Abstract]
Chen CY, Hung LY, Wu CS, Chuang TJ, Purifying selection shapes the coincident SNP distribution of primate coding sequences., Sci Rep, 06-03-2016 [Abstract]
Lindo J, Huerta-Sánchez E, Nakagome S, Rasmussen M, Petzelt B, Mitchell J, Cybulski JS, Willerslev E, DeGiorgio M, Malhi RS, A time transect of exomes from a Native American population before and after European contact., Nat Commun, 11-15-2016 [Abstract]
2015
Cocca, M., Pybus, M., Palamara, P.F., et al., Purging of deleterious variants due to drift and founder effect in Italian populations with extended autozygosity, bioRxiv, 10-12-2015 [Abstract]
Arunkumar R, Ness RW, Wright SI, Barrett SC, The evolution of selfing is accompanied by reduced efficacy of selection and purging of deleterious mutations., Genetics, 03-01-2015 [Abstract]
Hussin JG, Hodgkinson A, Idaghdour Y, Grenier JC, Goulet JP, Gbeha E, Hip-Ki E, Awadalla P, Recombination affects accumulation of damaging and disease-associated mutations in human populations., Nat Genet, 04-01-2015 [Abstract]
Douglas GM, Gos G, Steige KA, Salcedo A, Holm K, Josephs EB, Arunkumar R, Ågren JA, Hazzouri KM, Wang W, Platts AE, et al., Hybrid origins and the earliest stages of diploidization in the highly successful recent polyploid Capsella bursa-pastoris., Proc Natl Acad Sci U S A, 03-03-2015 [Abstract]
Bianco E, Soto HW, Vargas L, Pérez-Enciso M, The chimerical genome of Isla del Coco feral pigs (Costa Rica), an isolated population since 1793 but with remarkable levels of diversity., Mol Ecol, 05-01-2015 [Abstract]
Assaf ZJ, Petrov DA, Blundell JR, Obstruction of adaptation in diploids by recessive, strongly deleterious alleles., Proc Natl Acad Sci U S A, 05-19-2015 [Abstract]
Caballero A, Tenesa A, Keightley PD, The Nature of Genetic Variation for Complex Traits Revealed by GWAS and Regional Heritability Mapping Analyses., Genetics, 12-01-2015 [Abstract]
Mafessoni F, Lachmann M, Selective Strolls: Fixation and Extinction in Diploids Are Slower for Weakly Selected Mutations Than for Neutral Ones., Genetics, 12-01-2015 [Abstract]
Schrider DR, Kern AD, Inferring Selective Constraint from Population Genomic Data Suggests Recent Regulatory Turnover in the Human Brain., Genome Biol Evol, 11-19-2015 [Abstract]
2014
Enard D, Messer PW, Petrov DA, Genome-wide signals of positive selection in human evolution., Genome Res, 06-01-2014 [Abstract]
Veeramah KR, Gutenkunst RN, Woerner AE, Watkins JC, Hammer MF, Evidence for increased levels of positive and negative selection on the X chromosome versus autosomes in humans., Mol Biol Evol, 09-01-2014 [Abstract]
Comeron JM, Background selection as baseline for nucleotide variation across the Drosophila genome., PLoS Genet, 06-01-2014 [Abstract]
Bergland AO, Behrman EL, O'Brien KR, Schmidt PS, Petrov DA, Genomic evidence of rapid and stable adaptive oscillations over seasonal time scales in Drosophila., PLoS Genet, 11-01-2014 [Abstract]
2013
Kousathanas A, Keightley PD, A comparison of models to infer the distribution of fitness effects of new mutations., Genetics, 04-01-2013 [Abstract]
Messer PW, Petrov DA, Frequent adaptation and the McDonald-Kreitman test., Proc Natl Acad Sci U S A, 05-21-2013 [Abstract]