Simulation of genes and genomes forward in time

Current Genomics

Volumn 11, Issue 1, 2010, Pages 58-61

  Carvajal Rodríguez, Antonio ^a  

^a UNIVERSITY OF VIGO   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER MEMORY; COMPUTER PROGRAM; GENOME; GENOMICS; POPULATION GENETICS; PROTEOMICS; REVIEW; SIMULATION; SIMULATOR;

EID: 77950631483     PISSN: 13892029     EISSN: None     Source Type: Journal    
DOI: 10.2174/138920210790218007     Document Type: Review

References (35)

1. Di Ventura, B.; Lemerle, C.; Michalodimitrakis, K.; Serrano, L. From in vivo to in silico biology and back. Nature, 2006, 443, 527-533.
2. Mode, C.J.; Gallop, R.J. A review on Monte Carlo simulation methods as they apply to mutation and selection as formulated in Wright-Fisher models of evolutionary genetics. Math. Biosci., 2008, 211, 205-225.
3. Liu, Y.; Athanasiadis, G.; Weale, M.E. A survey of genetic simulation software for population and epidemiological studies. Hum. Genomics, 2008, 3, 79-86.
4. Carvajal-Rodriguez, A. Simulation of Genomes: A Review. Curr. Genomics, 2008, 9, 155-159.
5. Chadeau-Hyam, M.; Hoggart, C.; O'Reilly, P.; Whittaker, J.; De Iorio, M.; Balding, D. Fregene: Simulation of realistic sequence-level data in populations and ascertained samples. BMC Bioinformatics, 2008, 9, 364.
6. Lambert, B.W.; Terwilliger, J.D.; Weiss, K.M. ForSim: a tool for exploring the genetic architecture of complex traits with controlled truth. Bioinformatics, 2008, 24, 1821-1822.
7. Hernandez, R.D. A flexible forward simulator for populations subject to selection and demography. Bioinformatics, 2008, 24, 2786-2787.
8. Padhukasahasram, B.; Marjoram, P.; Wall, J.D.; Bustamante, C.D.; Nordborg, M. Exploring Population Genetic Models With Recombination Using Efficient Forward-Time Simulations. Genetics, 2008, 178, 2417-2427.
9. Carvajal-Rodriguez, A. GENOMEPOP: A program to simulate genomes in populations. BMC Bioinformatics, 2008, 9, 223.
10. Parreira, B.; Trussart, M.; Sousa, V.; Hudson, R.; Chikhi, L. SPAms: A user-friendly software to simulate population genetics data under complex demographic models. Mol. Ecol. Resour., 2009, 9, 749-753.
11. Chen, G.K.; Marjoram, P.; Wall, J.D. Fast and flexible simulation of DNA sequence data. Genome Res., 2009, 19, 136-142.
12. Varadarajan, A.; Bradley, R.K.; Holmes, I.H. Tools for simulating evolution of aligned genomic regions with integrated parameter estimation. Genome Biol., 2008, 9, R147.
13. Kim, Y.; Wiehe, T. Simulation of DNA sequence evolution under models of recent directional selection. Brief Bioinform, 2009, 10, 84-96.
14. Sommerville, I. Software engineering. 8th ed.; Addison-Wesley: Harlow, 2007; p. 840.
15. Cartwright, R.A. DNA assembly with gaps (Dawg): simulating sequence evolution. Bioinformatics, 2005, 21(Suppl 3), iii31-8.
16. Beiko, R.G.; Charlebois, R.L. A simulation test bed for hypotheses of genome evolution. Bioinformatics, 2007, 23, 825-831.
17. Marjoram, P.; Wall, J.D. Fast "coalescent" simulation. BMC Genet., 2006, 7, 16.
18. Teshima, K.; Innan, H. mbs: modifying Hudson's ms software to generate samples of DNA sequences with a biallelic site under selection. BMC Bioinformatics, 2009, 10, 166.
19. Kuo, C.H.; Janzen, F.J. Bottlesim: a bottleneck simulation program for long-lived species with overlapping generations. Mol. Ecol., 2003, 3, 669-673.
20. Balloux, F. EASYPOP (version 1.7): a computer program for population genetics simulations. J. Hered, 2001, 92, 301-302.
21. Hey, J. FPG: A computer program for forward population genetics simulation, 2004.
22. Strand, A.E.; Niehaus, J.M. kernelpop, a spatially explicit population genetic simulation engine. Mol. Ecol. Notes, 2007, 7, 969-973.
23. Guillaume, F.; Rougemont, J. Nemo: an evolutionary and population genetics programming framework. Bioinformatics, 2006, 22, 2556-2557.
24. R Development Core Team R: A language and environment for statistical computing, 2006. http://www.R-project.org
25. Sanford, J.; Baumgardner, J.; Brewer, W.; Gibson, P.; Remine, W. Mendel's Accountant: A biologically realistic forward-time population genetics program. SCPE, 2007, 8, 147-165.
26. Neuenschwander, S.; Hospital, F.; Guillaume, F.; Goudet, J. quantiNemo: an individual-based program to simulate quantitative traits with explicit genetic architecture in a dynamic metapopulation. Bioinformatics, 2008, 24, 1552-1553.
27. Peng, B.; Kimmel, M. simuPOP: a forward-time population genetics simulation environment. Bioinformatics, 2005, 21, 3686-3687.
28. Peng, B.; Amos, C. I. Forward-time Simulations of Nonrandom Mating Populations using simuPOP. Bioinformatics, 2009, 25, 1959-1960.
29. Strand, A. E. metasim 1.0: an individual-based environment for simulating population genetics of complex population dynamics. Mol. Ecol. Notes, 2002, 2, 373-376.
30. Control, E.B. f. S. S. a. Software Engineering Standards; 2; European Space Agency: 1991.
31. Jones, M.C.; Mortensen, U.K.; Fairclough, J. In The ESA Software Engineering Standards: Past, Present and Future, 3rd International Software Engineering Standards Symposium (ISESS '97), 1997, p. 119.
32. NVIDIA Corp NVIDIA CUDA (Compute Unified Device Architecture) Programming Guide, Version 1.0.; 2007.
33. Owens, J.D.; Luebke, D.; Govindaraju, N.; Harris, M.; Kruger, J.; Lefohn, A.E.; Purcell, T.J. A survey of general-purpose computation on graphics hardware. Comput. Graph. Forum, 2007, 26, 80-113.
34. Manavski, S.A.; Valle, G. CUDA compatible GPU cards as efficient hardware accelerators for Smith-Waterman sequence alignment. BMC Bioinformatics, 2008, 9(Suppl 2), S10.
35. Dynerman, D.; Butzlaff, E.; Mitchell, J.C. CUSA and CUDE: GPUAccelerated Methods for Estimating Solvent Accessible Surface Area and Desolvation. J. Comput. Biol., 2009, 16, 523-537.