WebAug 20, 2024 · The recombination sites predicted by Gubbins were excluded in the phylogeny ( Croucher et al., 2015 ). Pangenome SNP analysis was carried out using kSNP3.0 ( Gardner et al., 2015 ). The optimal size of the nucleotide regions flanking the SNPs (kmer) was identified using Kchooser available with the package. WebJul 14, 2024 · Multidrug-resistant Streptococcus pneumoniae emerge through the modification of core genome loci by interspecies homologous recombinations, and acquisition of gene cassettes. Both occurred in the otherwise contrasting histories of the antibiotic-resistant S. pneumoniae lineages PMEN3 and PMEN9.
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http://nickjcroucher.github.io/gubbins/#:~:text=Gubbins%20detects%20recombinations%20through%20the%20locally-elevated%20densities%20of,divergent%20from%20the%20set%20of%20sequences%20being%20analysed. WebGubbins (Genealogies Unbiased By recomBinations In Nucleotide Sequences) is an algorithm that iteratively identifies loci containing elevated densities of base substitutions … css key duties
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WebGubbins (Genealogies Unbiased By recomBinations In Nucleotide Sequences) is an algorithm that iteratively identifies loci containing elevated densities of base substitutions while concurrently constructing a phylogeny based on … WebCurrently, popular methods used for detecting recombination include Clon- alFrame (Didelot and Falush, 2007) and ClonalFrameML (Didelot and Wilson, 2015), Gubbins (Croucher et al., 2014b), and BratNextGen (Marttinen et al., 2012). WebIn David et al. (2024) PLOS Genetics, the numbers of recombination events were computed in two ways: first, the recent and ancestral recombinations as obtained from the fastGEAR output, and, second, by reconstructing the changes in the population structure, as estimated by fastGEAR, on a given tree, and reporting the number of times the … css keyboard shortcuts