To Tree or Not to Tree? Genome-Wide Quantification of Recombination and Reticulate Evolution during the Diversification of Strict Intracellular Bacteria

Evolving Concepts of Bacterial Species

(2012) Timothy G. Barraclough et al.   Evolutionary Biology

Phylo-MCOA: A Fast and Efficient Method to Detect Outlier Genes and Species in Phylogenomics Using Multiple Co-inertia Analysis

(2012) D. M. de Vienne et al.   MOLECULAR BIOLOGY AND EVOLUTION

Dendroscope 3: An Interactive Tool for Rooted Phylogenetic Trees and Networks

(2012) Daniel H. Huson et al.   SYSTEMATIC BIOLOGY

Detecting Phylogenetic Breakpoints and Discordance from Genome-Wide Alignments for Species Tree Reconstruction

(2011) Cécile Ané   Genome Biology and Evolution

Population structure in the Neisseria, and the biological significance of fuzzy species

(2011) J. Corander et al.   Journal of the Royal Society Interface

The Pfam protein families database

(2011) M. Punta et al.   NUCLEIC ACIDS RESEARCH

Neisseria meningitidis is structured in clades associated with restriction modification systems that modulate homologous recombination

(2011) S. Budroni et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Recombination and Population Structure in Salmonella enterica

(2011) Xavier Didelot et al.   PLoS Genetics

BUCKy: Gene tree/species tree reconciliation with Bayesian concordance analysis

(2010) Bret R. Larget et al.   BIOINFORMATICS

Rickettsial evolution in the light of comparative genomics

(2010) Vicky Merhej et al.   BIOLOGICAL REVIEWS

Harvesting Evolutionary Signals in a Forest of Prokaryotic Gene Trees

(2010) K. Schliep et al.   MOLECULAR BIOLOGY AND EVOLUTION

Networks of Gene Sharing among 329 Proteobacterial Genomes Reveal Differences in Lateral Gene Transfer Frequency at Different Phylogenetic Depths

(2010) T. Kloesges et al.   MOLECULAR BIOLOGY AND EVOLUTION

progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement

(2010) Aaron E. Darling et al.   PLoS One

Environmental Factors Determining the Epidemiology and Population Genetic Structure of the Bacillus cereus Group in the Field

(2010) Ben Raymond et al.   PLoS Pathogens

Prokaryotic evolution and the tree of life are two different things

(2009) Eric Bapteste et al.   Biology Direct

Evolution and diversity of Rickettsia bacteria

(2009) Lucy A Weinert et al.   BMC BIOLOGY

Pherotypes are driving genetic differentiation within Streptococcus pneumoniae

(2009) Margarida Carrolo et al.   BMC MICROBIOLOGY

Conjugative plasmids: vessels of the communal gene pool

(2009) A. Norman et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Genome Sequence of the Endosymbiont Rickettsia peacockii and Comparison with Virulent Rickettsia rickettsii: Identification of Virulence Factors

(2009) Roderick F. Felsheim et al.   PLoS One

The Dynamics and Time Scale of Ongoing Genomic Erosion in Symbiotic Bacteria

(2009) N. A. Moran et al.   SCIENCE

A comparison of homologous recombination rates in bacteria and archaea

(2008) Michiel Vos et al.   ISME Journal

Modular networks and cumulative impact of lateral transfer in prokaryote genome evolution

(2008) T. Dagan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA