SLiM: Simulating evolution with selection and linkage

Genetics

Volumn 194, Issue 4, 2013, Pages 1037-1039

  Messer, Philipp W ^a  

^a STANFORD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; BALANCING SELECTION; DEMOGRAPHY; EVOLUTION; EXON; GENE STRUCTURE; GENETIC VARIABILITY; HETEROZYGOSITY; HUMAN; MIGRATION; MUTATION; NOTE; POPULATION; POPULATION GENETICS; PRIORITY JOURNAL; REVERTANT; SELECTIVE SWEEP; SIMULATION; ARTICLE; CHROMOSOME; DIPLOIDY; GENE MAPPING; GENETIC LINKAGE; GENETIC SELECTION; GENETIC VARIATION; MOLECULAR EVOLUTION;

EID: 84881041428     PISSN: 00166731     EISSN: 19432631     Source Type: Journal    
DOI: 10.1534/genetics.113.152181     Document Type: Note

References (32)

1. Carvajal-Rodriguez, A., 2008 GENOMEPOP: a program to simulate genomes in populations. BMC Bioinformatics 9: 223.
2. Carvajal-Rodriguez, A., 2010 Simulation of genes and genomes forward in time. Curr. Genomics 11: 58-61.
3. Chadeau-Hyam, M., C. J. Hoggart, P. F. O'Reilly, J. C. Whittaker, M. De Iorio et al., 2008 Fregene: simulation of realistic sequencelevel data in populations and ascertained samples. BMC Bioinformatics 9: 364.
4. Ewing, G., and J. Hermisson, 2010 MSMS: a coalescent simulation program including recombination, demographic structure and selection at a single locus. Bioinformatics 26: 2064-2065.
5. Galassi, M., J. Davies, J. Theiler, B. Gough, G. Jungman et al., 2009 GNU Scientific Library: Reference Manual, Ed. 3. Network Theory, Bristol, UK.
6. Hernandez, R. D., 2008 A flexible forward simulator for populations subject to selection and demography. Bioinformatics 24: 2786-2787.
7. Hoban, S., G. Bertorelle, and O. E. Gaggiotti, 2011 Computer simulations: tools for population and evolutionary genetics. Nat. Rev. Genet. 13: 110-122.
8. Kousathanas, A., and P. D. Keightley, 2013 A comparison of models to infer the distribution of fitness effects of new mutations. Genetics 193: 1197-1208.
9. Lohmueller, K. E., A. Albrechtsen, Y. Li, S. Y. Kim, T. Korneliussen et al., 2011 Natural selection affects multiple aspects of genetic variation at putatively neutral sites across the human genome. PLoS Genet. 7: e1002326.
10. Messer, P. W., and D. A. Petrov, 2013 Frequent adaptation and the McDonald-Kreitman test. Proc. Natl. Acad. Sci. USA 110: 8615-8620.
11. Padhukasahasram, B., P. Marjoram, J. D. Wall, C. D. Bustamante, and M. Nordborg, 2008 Exploring population genetic models with recombination using efficient forward-time simulations. Genetics 178: 2417-2427.
12. Peng, B., and M. Kimmel, 2005 simuPOP: a forward-time population genetics simulation environment. Bioinformatics 21: 3686-3687.
13. Sella, G., D. A. Petrov, M. Przeworski, and P. Andolfatto, 2009 Pervasive natural selection in the Drosophila genome? PLoS Genet. 5: e1000495.
14. Weissman, D. B., and N. H. Barton, 2012 Limits to the rate of adaptive substitution in sexual populations. PLoS Genet. 8: e1002740.
15. Liu Y, Athanasiadis G, Weale ME (2008) A survey of genetic simulation software for population and epidemiological studies. Hum Genomics 3: 79-86.
16. Carvajal-Rodriguez A (2010) Simulation of genes and genomes forward in time. Curr Genomics 11: 58-61.
17. Hoban S, Bertorelle G, Gaggiotti OE (2011) Computer simulations: tools for population and evolutionary genetics. Nat Rev Genet 13: 110-122.
18. Ewing G, Hermisson J (2010) MSMS: a coalescent simulation program including recombination, demographic structure and selection at a single locus. Bioinformatics 26: 2064-2065.
19. Hernandez RD (2008) A exible forward simulator for populations subject to selection and demography. Bioinformatics 24: 2786-2787.
20. Chadeau-Hyam M, Hoggart CJ, O'Reilly PF, Whittaker JC, De Iorio M, et al. (2008) Fregene: simulation of realistic sequence-level data in populations and ascertained samples. BMC Bioinformatics 9: 364.
21. Padhukasahasram B, Marjoram P, Wall JD, Bustamante CD, Nordborg M (2008) Exploring population genetic models with recombination using efficient forward-time simulations. Genetics 178: 2417-2427.
22. Carvajal-Rodriguez A (2008) GENOMEPOP: a program to simulate genomes in populations. BMC Bioinformatics 9: 223.
23. Peng B, Kimmel M (2005) simuPOP: a forward-time population genetics simulation environment. Bioinformatics 21: 3686-3687.
24. Fisher R (1930) The genetical theory of natural selection. Oxford: Clarendon Press.
25. Charlesworth B, Charlesworth D (2010) Elements of Evolutionary Genetics. Greenwoord Village, Colorado, USA: Roberts and Company.
26. Galassi M, Davies J, Theiler J, Gough B, Jungman G, et al. (2009) GNU scientific library: Reference manual. Bristol,UK: Network Theory, 3rd edition.
27. Eyre-Walker A, Keightley PD (2007) The distribution of fitness effects of new mutations. Nat Rev Genet 8: 610-618.
28. L'Ecuyer P (1996) Maximally equidistributed combined tausworthe generators. Math Comput 65: 203-213.
29. Wakeley J (2008) Coalescent Theory: An Introduction. Greenwood Village, Colorado: Roberts & Company Publishers.
30. Charlesworth B (2009) Fundamental concepts in genetics: effective population size and patterns of molecular evolution and variation. Nat Rev Genet 10: 195-205.
31. Kimura M (1983) The Neutral Theory of Molecular Evolution. Cambridge: Cambridge University Press.
32. Barton NH (2000) Genetic hitchhiking. Philos Trans R Soc Lond, B, Biol Sci 355: 1553-1562.