Impact of homologous recombination on core genome phylogenies

CoreSimul: a forward-in-time simulator of genome evolution for prokaryotes modeling homologous recombination

(2020) Louis-Marie Bobay   BMC BIOINFORMATICS

Inferring bacterial recombination rates from large-scale sequencing datasets

(2019) Mingzhi Lin et al.   NATURE METHODS

Impact of Homologous Recombination on the Evolution of Prokaryotic Core Genomes

(2019) Pedro González-Torres et al.   mBio

A statistical method to identify recombination in bacterial genomes based on SNP incompatibility

(2018) Yi-Pin Lai et al.   BMC BIOINFORMATICS

Factors driving effective population size and pan-genome evolution in bacteria

(2018) Louis-Marie Bobay et al.   BMC EVOLUTIONARY BIOLOGY

Quantifying the risk of hemiplasy in phylogenetic inference

(2018) Rafael F. Guerrero et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Biological Species Are Universal across Life’s Domains

(2017) Louis-Marie Bobay et al.   Genome Biology and Evolution

Efficient Inference of Recent and Ancestral Recombination within Bacterial Populations

(2017) Rafal Mostowy et al.   MOLECULAR BIOLOGY AND EVOLUTION

Phylogenomics Reveals Three Sources of Adaptive Variation during a Rapid Radiation

(2016) James B. Pease et al.   PLOS BIOLOGY

Impermanence of bacterial clones

(2015) Louis-Marie Bobay et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fine-scale diversity and extensive recombination in a quasisexual bacterial population occupying a broad niche

(2015) M. J. Rosen et al.   SCIENCE

ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes

(2015) Xavier Didelot et al.   PLoS Computational Biology

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Genome-Wide Patterns of Recombination in the Opportunistic Human Pathogen Pseudomonas aeruginosa

(2014) Jeremy R. Dettman et al.   Genome Biology and Evolution

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

(2014) Nicholas J. Croucher et al.   NUCLEIC ACIDS RESEARCH

Extensive introgression in a malaria vector species complex revealed by phylogenomics

(2014) M. C. Fontaine et al.   SCIENCE

Whole-genome analyses resolve early branches in the tree of life of modern birds

(2014) E. D. Jarvis et al.   SCIENCE

Bacterial Phylogenetic Reconstruction from Whole Genomes Is Robust to Recombination but Demographic Inference Is Not

(2014) Jessica Hedge et al.   mBio

Mobile elements drive recombination hotspots in the core genome of Staphylococcus aureus

(2014) Richard G. Everitt et al.   Nature Communications

Impact of homologous and non-homologous recombination in the genomic evolution of Escherichia coli

(2012) Xavier Didelot et al.   BMC GENOMICS

Population Genomics of Early Events in the Ecological Differentiation of Bacteria

(2012) B. J. Shapiro et al.   SCIENCE

Impact of recombination on bacterial evolution

(2010) Xavier Didelot et al.   TRENDS IN MICROBIOLOGY

Organised Genome Dynamics in the Escherichia coli Species Results in Highly Diverse Adaptive Paths

(2009) Marie Touchon et al.   PLoS Genetics

Phylogenetic Inference Using Whole Genomes

(2008) Bruce Rannala et al.   Annual Review of Genomics and Human Genetics

A comparison of homologous recombination rates in bacteria and archaea

(2008) Michiel Vos et al.   ISME Journal

The Temporal Dynamics of Slightly Deleterious Mutations in Escherichia coli and Shigella spp.

(2008) K. J. Balbi et al.   MOLECULAR BIOLOGY AND EVOLUTION