ArticleMicrobial genomics2016
SimBac: simulation of whole bacterial genomes with homologous recombination.
Article in Microbial genomics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 44 citations in OpenAlex.
- A bacterial ecocline in Klebsiella pneumoniae may explain its backboned phylogeny.PLoS biology · 2026Article
- Genome co-adaptation and the evolution of methicillin resistant Staphylococcus aureus.Genome biology · 2026Article
- Article
- KPop: accurate and scalable comparative analysis of microbial genomes by sequence embeddings.Genome biology · 2025Article
- What Do We Gain When Tolerating Loss? The Information Bottleneck Wrings Out Recombination.Molecular biology and evolution · 2025Article
- SCARAP: scalable cross-species comparative genomics of prokaryotes.Bioinformatics (Oxford, England) · 2024Article
- Plasmid permissiveness of wastewater microbiomes can be predicted from 16S rRNA sequences by machine learning.Bioinformatics (Oxford, England) · 2023Article
- Current Methods for Recombination Detection in Bacteria.International journal of molecular sciences · 2022Review
- phastSim: Efficient simulation of sequence evolution for pandemic-scale datasets.PLoS computational biology · 2022Article
- Efficient ancestry and mutation simulation with msprime 1.0.Genetics · 2022Article
- phastSim: efficient simulation of sequence evolution for pandemic-scale datasets.bioRxiv : the preprint server for biology · 2021Article
- Accurate reconstruction of bacterial pan- and core genomes with PEPPAN.Genome research · 2020Article
- CoreSimul: a forward-in-time simulator of genome evolution for prokaryotes modeling homologous recombination.BMC bioinformatics · 2020Article
- Benchmarking bacterial genome-wide association study methods using simulated genomes and phenotypes.Microbial genomics · 2020Article
- PanDelos: a dictionary-based method for pan-genome content discovery.BMC bioinformatics · 2018Article
- GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens.Genome research · 2018Article
- Coalescent framework for prokaryotes undergoing interspecific homologous recombination.Heredity · 2018Article
- Bayesian reconstruction of transmission within outbreaks using genomic variants.PLoS computational biology · 2018Article
- SWPhylo - A Novel Tool for Phylogenomic Inferences by Comparison of Oligonucleotide Patterns and Integration of Genome-Based and Gene-Based Phylogenetic Trees.Evolutionary bioinformatics online · 2018Article
- The Bacterial Sequential Markov Coalescent.Genetics · 2017Article
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
Abstract
Bacteria can exchange genetic material, or acquire genes found in the environment. This process, generally known as bacterial recombination, can have a strong impact on the evolution and phenotype of bacteria, for example causing the spread of antibiotic resistance across clades and species, but can also disrupt phylogenetic and transmission inferences. With the increasing affordability of whole genome sequencing, the need has emerged for an efficient simulator of bacterial evolution to test and compare methods for phylogenetic and population genetic inference, and for simulation-based estimation. We present SimBac, a whole-genome bacterial evolution simulator that is roughly two orders of magnitude faster than previous software and includes a more general model of bacterial evolution, allowing both within- and between-species homologous recombination. Since methods modelling bacterial recombination generally focus on only one of these two modes of recombination, the possibility to simulate both allows for a general and fair benchmarking. SimBac is available from https://github.com/tbrown91/SimBac and is distributed as open source under the terms of the GNU General Public Licence.
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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.