ArticleFrontiers in genetics2013
Computer programs and methodologies for the simulation of DNA sequence data with recombination.
Article in Frontiers in genetics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
11 citing papers in PubMed, 18 citations in OpenAlex.
- wavess 1.2: Presenting an HLA-aware within-host virus sequence simulation framework.bioRxiv : the preprint server for biology · 2026Article
- wavess 1.2: presenting an HLA-aware within-host virus sequence simulation framework.Bioinformatics advances · 2026Article
- Consequences of Genetic Recombination on Protein Folding Stability.Journal of molecular evolution · 2023Article
- The Origin of Prebiotic Information System in the Peptide/RNA World: A Simulation Model of the Evolution of Translation and the Genetic Code.Life (Basel, Switzerland) · 2019Article
- Selecting among Alternative Scenarios of Human Evolution by Simulated Genetic Gradients.Genes · 2018Review
- The Bacterial Sequential Markov Coalescent.Genetics · 2017Article
- SimBac: simulation of whole bacterial genomes with homologous recombination.Microbial genomics · 2016Article
- Recombination in viruses: mechanisms, methods of study, and evolutionary consequences.Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2015Review
- Spatial and temporal simulation of human evolution. Methods, frameworks and applications.Current genomics · 2014Article
- Protein evolution along phylogenetic histories under structurally constrained substitution models.Bioinformatics (Oxford, England) · 2013Article
- The importance and application of the ancestral recombination graph.Frontiers in genetics · 2013Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
1 author at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Computer simulations are useful in evolutionary biology for hypothesis testing, to verify analytical methods, to analyze interactions among evolutionary processes, and to estimate evolutionary parameters. In particular, the simulation of DNA sequences with recombination may help in understanding the role of recombination in diverse evolutionary questions, such as the genome structure. Consequently, plenty of computer simulators have been developed to simulate DNA sequence data with recombination. However, the choice of an appropriate tool, among all currently available simulators, is critical if recombination simulations are to be biologically meaningful. This review provides a practical survival guide to commonly used computer programs and methodologies for the simulation of coding and non-coding DNA sequences with recombination. It may help in the correct design of computer simulation experiments of recombination. In addition, the study includes a review of simulation studies investigating the impact of ignoring recombination when performing various evolutionary analyses, such as phylogenetic tree and ancestral sequence reconstructions. Alternative analytical methodologies accounting for recombination are also reviewed.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.