Rapid forward-in-time simulation at the chromosome and genome level

BMC Bioinformatics

Volumn 14, Issue 1, 2013, Pages

  Aberer, Andre J ^a   Stamatakis, Alexandros ^a  

^a HEIDELBERG INSTITUTE FOR THEORETICAL STUDIES   (Germany)

Author keywords

Algorithm; Fisher Wright model; Forward in time simulation; Natural selection; Population genetics; Software

Indexed keywords

FISHER-WRIGHT MODEL; FORWARD SIMULATION; FORWARD-IN-TIME SIMULATION; FUNDAMENTAL TOOLS; NATURAL SELECTION; ORDERS OF MAGNITUDE; PERFORMANCE IMPROVEMENTS; POPULATION GENETICS;

ALGORITHMS; GENES; GRAPHIC METHODS; TOOLS; TRANSIENTS;

COMPUTER SOFTWARE;

ALGORITHM; ARTICLE; CHROMOSOME BREAKAGE; COMPUTER PROGRAM; COMPUTER SIMULATION; DOUBLE STRANDED DNA BREAK; EVOLUTION; GENETIC RECOMBINATION; GENETIC SELECTION; GENETICS; GENOME; MUTATION; NUCLEOTIDE SEQUENCE; POPULATION GENETICS; TIME;

ALGORITHMS; BASE SEQUENCE; BIOLOGICAL EVOLUTION; CHROMOSOME BREAKPOINTS; COMPUTER SIMULATION; DNA BREAKS, DOUBLE-STRANDED; GENETICS, POPULATION; GENOME; MUTATION; RECOMBINATION, GENETIC; SELECTION, GENETIC; SOFTWARE; TIME;

EID: 84880026546     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-14-216     Document Type: Article

References (30)

1. Liu DJ, Leal SM. Replication strategies for rare variant complex trait association studies via next-generation sequencing. Am J Hum Gen 2010, 87(6):790-801. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2997372&tool=pmcentrez&rendertype=abstract].
2. Abecasis GR, Auton A, Brooks LD, DePristo M, Durbin RM, Handsaker RE, Kang HM, Marth GT, McVean G. An integrated map of genetic variation from 1,092 human genomes. Nature 2012, 491(7422):56-65. [http://www.ncbi.nlm.nih.gov/pubmed/23128226], 10.1038/nature11632, 3498066, 23128226.
3. Pool JE, Hellmann I, Jensen JD, Nielsen R. Population genetic inference from genomic sequence variation. Genome Res 2010, 20(3):291-300. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2840988&tool=pmcentrez&rendertype=abstract], 10.1101/gr.079509.108, 2840988, 20067940.
4. Akey JM, Shriver MD. A grand challenge in evolutionary and population genetics: new paradigms for exploring the past and charting the future in the Post-genomic era. Front Genet 2011, 2(July):47. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3268600&tool=pmcentrez&rendertype=abstract], 3268600, 22303343.
5. Enard D, Depaulis F, Roest Crollius H. Human and non-human primate genomes share hotspots of positive selection. PLoS Genet 2010, 6(2):e1000840. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2816677&tool=pmcentrez&rendertype=abstract], 10.1371/journal.pgen.1000840, 2816677, 20140238.
6. Sinha P, Dincer A, Virgil D, Xu G, Poh YP, Jensen JD. On detecting selective sweeps using single genomes. Front Genet 2011, 2(December):85. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3268637&tool=pmcentrez&rendertype=abstract], 3268637, 22303379.
7. Li J, Li H, Jakobsson M, Li S, Sjödin P, Lascoux M. Joint analysis of demography and selection in population genetics: where do we stand and where could we go?. Mol Ecol 2012, 21:28-44. [http://www.ncbi.nlm.nih.gov/pubmed/21999307], 10.1111/j.1365-294X.2011.05308.x, 21999307.
8. Zhang W, Balding DJ, Beaumont Ma Approximate Bayesian computation in population genetics. Genetics 2002, 162(4):2025-2035. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1462356&tool=pmcentrez&rendertype=abstract], 1462356, 12524368, Beaumont Ma.
9. Hoban S, Bertorelle G, Gaggiotti OE. Computer simulations: tools for population and evolutionary genetics. Nat Rev Genet 2011, 13(2):110-122. [http://www.ncbi.nlm.nih.gov/pubmed/22230817].
10. Carvajal-Rodríguez A. Simulation of genes and genomes forward in time. Curr Genomics 2010, 11:58-61. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2851118&tool=pmcentrez&rendertype=abstract], 10.2174/138920210790218007, 2851118, 20808525.
11. Charlesworth B. Fundamental concepts in genetics: effective population size and patterns of molecular evolution and variation. Nat Rev Genet 2009, 10(3):195-205. [http://www.ncbi.nlm.nih.gov/pubmed/19204717], 10.1038/nrg2526, 19204717.
12. Hudson RR. Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics (Oxford, England) 2002, 18(2):337-338. [http://www.ncbi.nlm.nih.gov/pubmed/11847089].
13. Cardin NJ, McVean GaT Approximating the coalescent with recombination. Philos Trans R Soc Lond B Biol Sci 2005, 360(1459):1387-1393. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1569517&tool=pmcentrez&rendertype=abstract], 10.1098/rstb.2005.1673, 1569517, 16048782, McVean GaT.
14. Spencer C, Coop G. SelSim: a program to simulate population genetic data with natural selection and recombination. Bioinformatics (Oxford, England) 2004, 20(18):3673-3675. [http://www.ncbi.nlm.nih.gov/pubmed/15271777].
15. Ewing G, Hermisson J. MSMS: a coalescent simulation program including recombination, demographic structure and selection at a single locus. Bioinformatics (Oxford, England) 2010, 26(16):2064-2065. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2916717&tool=pmcentrez&rendertype=abstract].
16. Chadeau-Hyam M, Hoggart CJ, O'Reilly PF, Whittaker JC, De, Iorio M, Balding DJ. Fregene: simulation of realistic sequence-level data in populations and ascertained samples. BMC Bioinformatics 2008, 9:364. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2542380&tool=pmcentrez&rendertype=abstract], 10.1186/1471-2105-9-364, 2542380, 18778480.
17. Kim Y, Wiehe T. Simulation of DNA sequence evolution under models of recent directional selection. Brief Bioinform 2009, 10:84-96. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2638626&tool=pmcentrez&rendertype=abstract], 2638626, 19109303.
18. Padhukasahasram B, Marjoram P, Wall JD, Bustamante CD, Nordborg M. Exploring population genetic models with recombination using efficient forward-time simulations. Genetics 2008, 178(4):2417-2427. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2323826&tool=pmcentrez&rendertype=abstract], 10.1534/genetics.107.085332, 2323826, 18430959.
19. Doroghazi JR, Buckley DH. A model for the effect of homologous recombination on microbial diversification. Genome Biol Evol 2011, 3:1349-1356. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3240962&tool=pmcentrez&rendertype=abstract], 10.1093/gbe/evr110, 3240962, 22071790.
20. Eyre-Walker A, Keightley PD. The distribution of fitness effects of new mutations. Nature Rev Genet 2007, 8(8):610-618. [http://www.ncbi.nlm.nih.gov/pubmed/17637733].
21. Hernandez RD. A flexible forward simulator for populations subject to selection and demography. Bioinformatics (Oxford, England) 2008, 24(23):2786-2787. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2639268&tool=pmcentrez&rendertype=abstract].
22. Matsumoto M, Nishimura T. Mersenne twister: a 623-dimensionally equidistributed uniform pseudo-random number generator. ACM Trans Model Comput Simul 1998, 8:3-30. [http://portal.acm.org/citation.cfm?doid=272991.272995].
23. Saito M, Matsumoto M. SIMD-oriented fast mersenne twister: a 128-bit pseudorandom number generator. Monte Carlo and Quasi-Monte Carlo Methods 2006 2008, 607-622. Berlin, Heidelberg: Springer.
24. Karney C [http://randomlib.sourceforge.net/] 2011, Karney C.
25. Peng B, Kimmel M. simuPOP: a forward-time population genetics simulation environment. Bioinformatics (Oxford, England) 2005, 21(18):3686-3687. [http://www.ncbi.nlm.nih.gov/pubmed/16020469].
26. Baskins D. [http://judy.sourceforge.net/] 2004.
27. Nachman MW, Crowell SL. Estimate of the mutation rate per nucleotide in humans. Genetics 2000, 156:297-304. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1461236&tool=pmcentrez&rendertype=abstract], 1461236, 10978293.
28. Jensen-Seaman MI, Furey TS, Payseur B, Lu Y, Roskin KM, Chen CF, Haussler D, Jacob HJ, Thomas Ma Comparative recombination rates in the rat, mouse, and human genomes. Genome Res 2004, 14(4):528-538. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=383296&tool=pmcentrez&rendertype=abstract], 10.1101/gr.1970304, 383296, 15059993, Thomas Ma.
29. Hernandez RD. SFS_Code. 2012, [http://sfscode.sourceforge.net/SFS\_CODE/].
30. Freedman D, Diaconis P. On the histogram as a density estimator:L 2 theory. Probability Theory Relat Fields 1981, 57(4):453-476. [http://www.springerlink.com/index/10.1007/BF01025868].