ArticlePLoS computational biology2018
MimicrEE2: Genome-wide forward simulations of Evolve and Resequencing studies.
Article in PLoS computational biology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed.
- Intersecting experimental evolution and CRISPR screens to identify novel toxin resistance loci.eLife · 2026Article
- The Genetic Architecture of Venom Resistance: A Novel Approach to Target Identification and Coevolutionary Discovery.Molecular biology and evolution · 2026Article
- Pollution-Driven Selection in a Non-Biting Midge: Genome-Wide Responses to Bacillus thuringiensis israelensis and Copper.Molecular ecology · 2026Article
- Unraveling Epistatic Interactions Between Sites Under Drug-Dependent Selection in the Mycobacterium tuberculosis Genome.Molecular biology and evolution · 2025Article
- Pleiotropy increases parallel selection signatures during adaptation from standing genetic variation.eLife · 2025Article
- Evolution of Phenotypic Variance Provides Insights into the Genetic Basis of Adaptation.Genome biology and evolution · 2024Article
- Haplotype based testing for a better understanding of the selective architecture.BMC bioinformatics · 2023Article
- SLiM 4: Multispecies Eco-Evolutionary Modeling.The American naturalist · 2023Article
- Article
- Bait-ER: A Bayesian method to detect targets of selection in Evolve-and-Resequence experiments.Journal of evolutionary biology · 2023Article
- Genome-wide selection signatures reveal widespread synergistic effects of two different stressors inProceedings. Biological sciences · 2022Article
- Genome-wide signatures of synergistic epistasis during parallel adaptation in a Baltic Sea copepod.Nature communications · 2022Article
- Natural variation in Drosophila shows weak pleiotropic effects.Genome biology · 2022Article
- Highly Parallel Genomic Selection Response in Replicated Drosophila melanogaster Populations with Reduced Genetic Variation.Genome biology and evolution · 2021Article
- The genetic architecture of temperature adaptation is shaped by population ancestry and not by selection regime.Genome biology · 2021Article
- Episodic evolution of coadapted sets of amino acid sites in mitochondrial proteins.PLoS genetics · 2021Article
- Detecting selected haplotype blocks in evolve and resequence experiments.Molecular ecology resources · 2021Article
- The Effects of Quantitative Trait Architecture on Detection Power in Short-Term Artificial Selection Experiments.G3 (Bethesda, Md.) · 2020Article
- Low concordance of short-term and long-term selection responses in experimental Drosophila populations.Molecular ecology · 2020Article
- Distinct Patterns of Selective Sweep and Polygenic Adaptation in Evolve and Resequence Studies.Genome biology and evolution · 2020Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
Evolve and Resequencing (E&R) studies allow us to monitor adaptation at the genomic level. By sequencing evolving populations at regular time intervals, E&R studies promise to shed light on some of the major open questions in evolutionary biology such as the repeatability of evolution and the molecular basis of adaptation. However, data interpretation, statistical analysis and the experimental design of E&R studies increasingly require simulations of evolving populations, a task that is difficult to accomplish with existing tools, which may i) be too slow, ii) require substantial reformatting of data, iii) not support an adaptive scenario of interest or iv) not sufficiently capture the biology of the used model organism. Therefore we developed MimicrEE2, a multi-threaded Java program for genome-wide forward simulations of evolving populations. MimicrEE2 enables the convenient usage of available genomic resources, supports biological particulars of model organism frequently used in E&R studies and offers a wide range of different adaptive models (selective sweeps, polygenic adaptation, epistasis). Due to its user-friendly and efficient design MimicrEE2 will facilitate simulations of E&R studies even for small labs with limited bioinformatics expertise or computational resources. Additionally, the scripts provided for executing MimicrEE2 on a computer cluster permit the coverage even of a large parameter space. MimicrEE2 runs on any computer with Java installed. It is distributed under the GPLv3 license at https://sourceforge.net/projects/mimicree2/.
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