title: Simulation of genes and genomes forward in time.
abstract: The importance of simulation software in current and future evolutionary and genomic studies is just confirmed by the recent publication of several new simulation tools. The forward-in-time simulation strategy has, therefore, re-emerged as a complement of coalescent simulation. Additionally, more efficient coalescent algorithms, the same as new ideas about the combined use of backward and forward strategies have recently appeared. In the present work, a previous review is updated to include some new forward simulation tools. When simulating at the genome-scale the conflict between efficiency (i.e. execution speed and memory usage) and flexibility (i.e. complex modeling capabilities) emerges. This is the pivot around which simulation of evolutionary processes should improve. In addition, some effort should be made to consider the process of developing simulation tools from the point of view of the software engineering theory. Finally, some new ideas and technologies as general purpose graphic processing units are commented.
authors.affiliation: Departamento de Bioquímica, Genética e Inmunología, Universidad de Vigo, 36310 Vigo, Spain.
authors.forename: Antonio
authors.initials: A
authors.lastname: Carvajal-Rodríguez
references.citation: BMC Bioinformatics. 2008 Mar 26;9 Suppl 2:S10
references.pmid: 18387198
references.citation: J Hered. 2001 May-Jun;92(3):301-2
references.pmid: 11447253
references.citation: BMC Bioinformatics. 2008 Apr 30;9:223
references.pmid: 18447924
references.citation: Bioinformatics. 2008 Aug 15;24(16):1821-2
references.pmid: 18565989
references.citation: Bioinformatics. 2008 Dec 1;24(23):2786-7
references.pmid: 18842601
references.citation: Brief Bioinform. 2009 Jan;10(1):84-96
references.pmid: 19109303
references.citation: Nature. 2006 Oct 5;443(7111):527-33
references.pmid: 17024084
references.citation: Mol Ecol Resour. 2009 May;9(3):749-53
references.pmid: 21564735
references.citation: Bioinformatics. 2007 Apr 1;23(7):825-31
references.pmid: 17267425
references.citation: Bioinformatics. 2005 Nov 1;21 Suppl 3:iii31-8
references.pmid: 16306390
references.citation: Bioinformatics. 2005 Sep 15;21(18):3686-7
references.pmid: 16020469
references.citation: Genome Res. 2009 Jan;19(1):136-42
references.pmid: 19029539
references.citation: Genetics. 2008 Apr;178(4):2417-27
references.pmid: 18430959
references.citation: Bioinformatics. 2008 Jul 1;24(13):1552-3
references.pmid: 18450810
references.citation: Curr Genomics. 2008 May;9(3):155-9
references.pmid: 19440512
references.citation: Bioinformatics. 2008 Jun 1;24(11):1408-9
references.pmid: 18417488
references.citation: BMC Bioinformatics. 2008 Sep 08;9:364
references.pmid: 18778480
references.citation: Genome Biol. 2008 Oct 08;9(10):R147
references.pmid: 18840304
references.citation: Bioinformatics. 2006 Oct 15;22(20):2556-7
references.pmid: 16882649
references.citation: Hum Genomics. 2008 Sep;3(1):79-86
references.pmid: 19129092
references.citation: BMC Bioinformatics. 2009 May 30;10:166
references.pmid: 19480708
references.citation: Math Biosci. 2008 Feb;211(2):205-25
references.pmid: 18190932
references.citation: J Comput Biol. 2009 Apr;16(4):523-37
references.pmid: 19361325
references.citation: BMC Genet. 2006 Mar 15;7:16
references.pmid: 16539698