FFPopSim: an efficient forward simulation package for the evolution of large populations

Zanini, Fabio and Neher, Richard A.. (2012) FFPopSim: an efficient forward simulation package for the evolution of large populations. Bioinformatics, 28 (24). pp. 3332-3333.

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Official URL: http://edoc.unibas.ch/53993/

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The analysis of the evolutionary dynamics of a population with many polymorphic loci is challenging, as a large number of possible genotypes needs to be tracked. In the absence of analytical solutions, forward computer simulations are an important tool in multi-locus population genetics. The run time of standard algorithms to simulate sexual populations increases as 8(L) with the number of loci L, or with the square of the population size N.; We have developed algorithms to simulate large populations with arbitrary genetic maps, including multiple crossovers, with a run time that scales as 3(L). If the number of crossovers is restricted to at most one, the run time is reduced to L2(L). The algorithm is based on an analogue of the Fast Fourier Transform (FFT) and allows for arbitrary fitness functions (i.e. any epistasis). In addition, we include a streamlined individual-based framework. The library is implemented as a collection of C++ classes and a Python interface.
Faculties and Departments:05 Faculty of Science > Departement Biozentrum > Computational & Systems Biology > Computational Modeling of Biological Processes (Neher)
UniBasel Contributors:Neher, Richard
Item Type:Article, refereed
Article Subtype:Research Article
Publisher:Oxford University Press
Note:Publication type according to Uni Basel Research Database: Journal article
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Last Modified:18 Sep 2019 05:30
Deposited On:30 Nov 2017 11:19

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