ArticleBMC bioinformatics2020
CoreSimul: a forward-in-time simulator of genome evolution for prokaryotes modeling homologous recombination.
Article in BMC bioinformatics, 2020. 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
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
11 citing papers in PubMed.
- Article
- Introgression impacts the evolution of bacteria, but species borders are rarely fuzzy.Nature communications · 2025Article
- Homologous recombination shapes the architecture and evolution of bacterial genomes.Nucleic acids research · 2025Article
- Homologous Recombination Shapes the Architecture and Evolution of Bacterial Genomes.bioRxiv : the preprint server for biology · 2024Article
- Evolution of homologous recombination rates across bacteria.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Rhometa: Population recombination rate estimation from metagenomic read datasets.PLoS genetics · 2023Article
- Gene flow and introgression are pervasive forces shaping the evolution of bacterial species.Genome biology · 2022Article
- Current Methods for Recombination Detection in Bacteria.International journal of molecular sciences · 2022Review
- Recombination events are concentrated in the spike protein region of Betacoronaviruses.PLoS genetics · 2020Article
- Impact of homologous recombination on core genome phylogenies.BMC genomics · 2020Article
- Strain Structure and Dynamics Revealed by Targeted Deep Sequencing of the Honey Bee Gut Microbiome.mSphere · 2020Article
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.
Funding
Abstract
backgroundProkaryotes are asexual, but these organisms frequently engage in homologous recombination, a process that differs from meiotic recombination in sexual organisms. Most tools developed to simulate genome evolution either assume sexual reproduction or the complete absence of DNA flux in the population. As a result, very few simulators are adapted to model prokaryotic genome evolution while accounting for recombination. Moreover, many simulators are based on the coalescent, which assumes a neutral model of genomic evolution, and those are best suited for organisms evolving under weak selective pressures, such as animals and plants. In contrast, prokaryotes are thought to be evolving under much stronger selective pressures, suggesting that forward-in-time simulators are better suited for these organisms.
resultsHere, I present CoreSimul, a forward-in-time simulator of core genome evolution for prokaryotes modeling homologous recombination. Simulations are guided by a phylogenetic tree and incorporate different substitution models, including models of codon selection.
conclusionsCoreSimul is a flexible forward-in-time simulator that constitutes a significant addition to the limited list of available simulators applicable to prokaryote genome evolution.
Indexed as
Identifiers
What OpenQuestion holds
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.