Inference of Bacterial Microevolution Using Multilocus Sequence Data

By Xavier Didelot, Daniel Falush. Genetics, 2007

682 citations recorded by the source corpus.

Subfields: Endocrinology, Food Science, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/46d5695d50551785b234d5730e7fdf94f59135d8

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Citations in the corpus

Multilocus Sequence Typing as a Replacement for Serotyping in Salmonella enterica (2012, methodology): “Concatenated sequences from all seven gene fragments within 1092 STs were aligned using Mega 4 [96] and analyzed by ClonalFrame [51], yielding the tree in Fig.”
Characterization of Pseudomonas syringae pv. actinidiae (Psa) isolated from France and assignment of Psa biovar 4 to a de novo pathovar: Pseudomonas syringae pv. actinidifoliorum pv. nov. (2015, methodology): “In order to estimate the clonal genealogy of the four biovars of Psa, CLONALFRAME software (Didelot & Falush, 2007) was used.”
BIGSdb: Scalable analysis of bacterial genome variation at the population level (2010, methodology): “Other formats include extended multi-FASTA where data for each locus are grouped in aligned blocks, facilitating whole genome phylogenetic analysis with applications such as ClonalFrame [24].”
progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement (2010, methodology): “The positional homology alignment facilitates downstream alignment tasks such as phylogenetic inference of nucleotide substitution, phylogenetic inference of gene gain and loss [55], phylogenetic inference of rearrangement [64], and even inference of homologous recombination-induced lateral gene tra”
Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins (2014, methodology): “The most sophisticated software available to implement this approach is ClonalFrame (19), which uses a Bayesian Monte Carlo Markov chain (MCMC) approach to detect recombinations as regions with a significantly elevated density of polymorphisms while simultaneously constructing a tree based on the po”
ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes (2015, methodology): “The ClonalFrame software [44] attempts to reconstruct this tree of clonal relationships between isolates by detecting the location of recombined regions on each branch.”
Ribosomal Multi-Locus Sequence Typing: universal characterisation of bacteria from domain to strain (2012, methodology): “While 16S rRNA gene phylogenies provide a general framework, they are unable to provide unification between taxonomic and typing schemes, as many bacteria with distinct properties share identical or very similar 16S rRNA gene sequences (Stackebrandt et al., 2002).”