(Q35559913)

8 August 2017

title

ClonalFrameML: efficient inference of recombination in whole bacterial genomes (English)

1 reference

8 August 2017

1

0 references

author name string

Daniel J Wilson

series ordinal

2

1 reference

8 August 2017

publication date

12 February 2015

1 reference

PLOS Computational Biology

8 August 2017

published in

1 reference

8 August 2017

volume

11

1 reference

8 August 2017

issue

2

1 reference

8 August 2017

page(s)

e1004041

1 reference

Creative Commons Attribution 4.0 International

8 August 2017

copyright license

start time

12 February 2015

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

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12 July 2018

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12 July 2018

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12 July 2018

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12 July 2018

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12 July 2018

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Subpopulations of Staphylococcus aureus clonal complex 121 are associated with distinct clinical entities

12 July 2018

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Chromosome painting in silico in a bacterial species reveals fine population structure

12 July 2018

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A genomic portrait of the emergence, evolution, and global spread of a methicillin-resistant Staphylococcus aureus pandemic

12 July 2018

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Progressive genome-wide introgression in agricultural Campylobacter coli

12 July 2018

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12 July 2018

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Microevolutionary analysis of Clostridium difficile genomes to investigate transmission

12 July 2018

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Recombinational switching of the Clostridium difficile S-layer and a novel glycosylation gene cluster revealed by large-scale whole-genome sequencing

12 July 2018

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12 July 2018

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Whole-genome sequencing to delineate Mycobacterium tuberculosis outbreaks: a retrospective observational study

12 July 2018

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12 July 2018

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Transforming clinical microbiology with bacterial genome sequencing.

12 July 2018

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Comparative transcriptional analysis of clinically relevant heat stress response in Clostridium difficile strain 630.

12 July 2018

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12 July 2018

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12 July 2018

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12 July 2018

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Pneumococcal genome sequencing tracks a vaccine escape variant formed through a multi-fragment recombination event

12 July 2018

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12 July 2018

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12 July 2018

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Evidence for several waves of global transmission in the seventh cholera pandemic

12 July 2018

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Helicobacter pylori genome evolution during human infection

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4326465

Rapid pneumococcal evolution in response to clinical interventions

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4326465

Inference of homologous recombination in bacteria using whole-genome sequences

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4326465

New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4326465

Impact of recombination on bacterial evolution

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4326465

FastTree 2--approximately maximum-likelihood trees for large alignments

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4326465

Evolution of MRSA during hospital transmission and intercontinental spread

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4326465

Genome sequence of a recently emerged, highly transmissible, multi-antibiotic- and antiseptic-resistant variant of methicillin-resistant Staphylococcus aureus, sequence type 239 (TW).

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4326465

Genealogical typing of Neisseria meningitidis.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4326465

SimMLST: simulation of multi-locus sequence typing data under a neutral model

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4326465

The peopling of the Pacific from a bacterial perspective

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4326465

Rapid evolution and the importance of recombination to the gastroenteric pathogen Campylobacter jejuni

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4326465

BEAST: Bayesian evolutionary analysis by sampling trees

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4326465

Recombination and the nature of bacterial speciation

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4326465

Inference of bacterial microevolution using multilocus sequence data

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4326465

RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4326465

The multidrug-resistant human pathogen Clostridium difficile has a highly mobile, mosaic genome

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4326465

A simple and robust statistical test for detecting the presence of recombination

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4326465

Evolution of Staphylococcus aureus by large chromosomal replacements.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4326465

Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4326465

Traces of human migrations in Helicobacter pylori populations

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4326465

A coalescent-based method for detecting and estimating recombination from gene sequences

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4326465

The effect of recombination on the accuracy of phylogeny estimation

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4326465

Consequences of recombination on traditional phylogenetic analysis.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4326465

A fast algorithm for joint reconstruction of ancestral amino acid sequences

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4326465

Lateral gene transfer and the nature of bacterial innovation

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4326465

The coalescent with gene conversion

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4326465

Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4326465

A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4326465

Dating of the human-ape splitting by a molecular clock of mitochondrial DNA

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4326465

Molecular evolution of the Escherichia coli chromosome. III. Clonal frames

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4326465

MLST revisited: the gene-by-gene approach to bacterial genomics.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4326465

Determination of the attP and attB sites of phage CD27 from Clostridium difficile NCTC 12727.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4326465

Recombination and clonality in natural populations of Escherichia coli.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4326465

A comparison of homologous recombination rates in bacteria and archaea.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4326465

Convergence of Campylobacter species: implications for bacterial evolution.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4326465

A bimodal pattern of relatedness between the Salmonella Paratyphi A and Typhi genomes: convergence or divergence by homologous recombination?

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4326465

Approximating the coalescent with recombination

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4326465

The influence of mutation, recombination, population history, and selection on patterns of genetic diversity in Neisseria meningitidis

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4326465

Clonal divergence in Escherichia coli as a result of recombination, not mutation

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4326465

Recombination and the molecular clock

26 September 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25675341

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PCBI.1004041

1 reference

journals/ploscb/DidelotW15

8 August 2017

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

release_yqff2pqijvbkdklq236zihekry

28 January 2021

Fatcat ID

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/yqff2pqijvbkdklq236zihekry

mapped directly with Wikidata item

24 November 2022

based on heuristic

PMC publication ID

4326465

1 reference

8 August 2017

1 reference