Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
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Summary
Gubbins is an iterative algorithm that uses spatial scanning statistics to identify loci containing elevated densities of base substitutions suggestive of horizontal sequence transfer while concurrently constructing a maximum likelihood phylogeny based on the putative point mutations outside these regions of high sequence diversity.
- Type
- article
- Published
- 2014-11-20
- Cited by
- 2,505
- References
- 60
- Access
- Open access
- OpenAlex
- https://openalex.org/W1972145956
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:14587670
Keywords
Biology, Python (programming language), Genome, Phylogenetic tree, Bacterial genome size
References
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- Genomic Characterisation of Invasive Non-Typhoidal Salmonella enterica Subspecies enterica Serovar Bovismorbificans Isolates from Malawi
- Detecting Evolutionary Incompatibilities From Protein Sequences
- progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement
- Effect of chromosome location on bacterial mutation rates.
- Evidence for multiple waves of global transmission within the seventh cholera pandemic
- Localized sex in bacteria
- Dominant Role of Nucleotide Substitution in the Diversification of Serotype 3 Pneumococci over Decades and during a Single Infection
- Comparison of phylogenetic trees
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- A Primer on Infectious Disease Bacterial Genomics
- Topical Antibiotic Use Coselects for the Carriage of Mobile Genetic Elements Conferring Resistance to Unrelated Antimicrobials in Staphylococcus aureus
- Emergence of an Extensively Drug-Resistant Salmonella enterica Serovar Typhi Clone Harboring a Promiscuous Plasmid Encoding Resistance to Fluoroquinolones and Third-Generation Cephalosporins
- Whole-genome sequencing in the investigation of recurrent invasive group A streptococcus outbreaks in a maternity unit.
- Genome-based epidemiology and antimicrobial resistance determinants of Neisseria gonorrhoeae isolates with decreased susceptibility and resistance to extended-spectrum cephalosporins in Argentina in 2011-16.
- Microevolution of antimicrobial resistance and biofilm formation of Salmonella Typhimurium during persistence on pig farms
- Molecular Characteristics of an NDM-4 and OXA-181 Co-Producing K51-ST16 Carbapenem-Resistant Klebsiella pneumoniae: Study of Its Potential Dissemination Mediated by Conjugative Plasmids and Insertion Sequences
- Genomics tools in microbial food safety
- Development of a Multilocus Sequence Typing Scheme for Molecular Typing of Mycoplasma pneumoniae
- The population genetics of pathogenic Escherichia coli
- High multiple carriage and emergence of Streptococcus pneumoniae vaccine serotype variants in Malawian children
- Genetic diversity in the plasticity zone and the presence of the chlamydial plasmid differentiates Chlamydia pecorum strains from pigs, sheep, cattle, and koalas
- Whole-Genome Sequencing Allows for Improved Identification of Persistent Listeria monocytogenes in Food-Associated Environments
- Evolutionary dynamics of methicillin-resistant Staphylococcus aureus within a healthcare system
- Mechanisms and impact of genetic recombination in the evolution of Streptococcus pneumoniae
- Selective and Genetic Constraints on Pneumococcal Serotype Switching
- Emergence of a New Highly Successful Acapsular Group A Streptococcus Clade of Genotype emm89 in the United Kingdom
- Origin and Proliferation of Multiple-Drug Resistance in Bacterial Pathogens
- A high-resolution genomic analysis of multidrug-resistant hospital outbreaks of Klebsiella pneumoniae
- Species-wide whole genome sequencing reveals historical global spread and recent local persistence in Shigella flexneri
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