ArticleBioinformatics (Oxford, England)2012
FFPopSim: an efficient forward simulation package for the evolution of large populations.
Article in Bioinformatics (Oxford, England), 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- Article
- Genomic surveillance uncovers a pandemic clonal lineage of the wheat blast fungus.PLoS biology · 2023Article
- Conflicting effects of recombination on the evolvability and robustness in neutrally evolving populations.PLoS computational biology · 2022Review
- Genomic epidemiological models describe pathogen evolution across fitness valleys.Science advances · 2022Article
- Article
- Evolution during primary HIV infection does not require adaptive immune selection.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Limited Predictability of Amino Acid Substitutions in Seasonal Influenza Viruses.Molecular biology and evolution · 2021Article
- The Effects of Quantitative Trait Architecture on Detection Power in Short-Term Artificial Selection Experiments.G3 (Bethesda, Md.) · 2020Article
- Inferring population genetics parameters of evolving viruses using time-series data.Virus evolution · 2019Article
- SANTA-SIM: simulating viral sequence evolution dynamics under selection and recombination.Virus evolution · 2019Article
- The G-matrix Simulator Family: Software for Research and Teaching.The Journal of heredity · 2018Article
- MimicrEE2: Genome-wide forward simulations of Evolve and Resequencing studies.PLoS computational biology · 2018Article
- TreeTime: Maximum-likelihood phylodynamic analysis.Virus evolution · 2018Article
- Estimating virus effective population size and selection without neutral markers.PLoS pathogens · 2017Article
- OncoSimulR: genetic simulation with arbitrary epistasis and mutator genes in asexual populations.Bioinformatics (Oxford, England) · 2017Article
- Within-Epitope Interactions Can Bias CTL Escape Estimation in Early HIV Infection.Frontiers in immunology · 2017Article
- Investigating the Consequences of Interference between Multiple CD8+ T Cell Escape Mutations in Early HIV Infection.PLoS computational biology · 2016Article
- Emergence of terpene cyclization in Artemisia annua.Nature communications · 2015Article
- Article
- Multidimensional epistasis and the transitory advantage of sex.PLoS computational biology · 2014Article
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2 authors.
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Abstract
motivationThe 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.
resultsWe 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.
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