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Open Access Methodology article

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

Andre J Aberer* and Alexandros Stamatakis

Author Affiliations

The Exelixis Lab, Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, Heidelberg D-69118, Germany

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BMC Bioinformatics 2013, 14:216  doi:10.1186/1471-2105-14-216

Published: 9 July 2013

Abstract

Background

In population genetics, simulation is a fundamental tool for analyzing how basic evolutionary forces such as natural selection, recombination, and mutation shape the genetic landscape of a population. Forward simulation represents the most powerful, but, at the same time, most compute-intensive approach for simulating the genetic material of a population.

Results

We introduce AnA-FiTS, a highly optimized forward simulation software, that is up to two orders of magnitude faster than current state-of-the-art software. In addition, we present a novel algorithm that further improves runtimes by up to an additional order of magnitude, for simulations where a fraction of the mutations is neutral (e.g., only 10% of mutations have an effect on fitness). Apart from simulated sequences, our tool also generates a graph structure that depicts the complete observable history of neutral mutations.

Conclusions

The substantial performance improvements allow for conducting forward simulations at the chromosome and genome level. The graph structure generated by our algorithm can give rise to novel approaches for visualizing and analyzing the output of forward simulations.

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