Telling the whole story in a 10,000-genome world

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Assembling networks of microbial genomes using linear programming

(2010) Catherine Holloway et al.   BMC EVOLUTIONARY BIOLOGY

On the artefactual parasitic eubacteria clan in conditioned logdet phylogenies: heterotachy and ortholog identification artefacts as explanations

(2010) Ajanthah Sangaralingam et al.   BMC EVOLUTIONARY BIOLOGY

Analysis and comparison of the pan-genomic properties of sixteen well-characterized bacterial genera

(2010) Brett Trost et al.   BMC MICROBIOLOGY

A Survey of Combinatorial Methods for Phylogenetic Networks

(2010) Daniel H. Huson et al.   Genome Biology and Evolution

Genome Networks Root the Tree of Life between Prokaryotic Domains

(2010) Tal Dagan et al.   Genome Biology and Evolution

The Tree and Net Components of Prokaryote Evolution

(2010) Pere Puigbò et al.   Genome 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

OMA 2011: orthology inference among 1000 complete genomes

(2010) A. M. Altenhoff et al.   NUCLEIC ACIDS RESEARCH

Evolutionary dynamics of Clostridium difficile over short and long time scales

(2010) M. He et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phylogeny, diversity and host specialization in the phylum Synergistetes with emphasis on strains and clones of human origin

(2010) Hélène Marchandin et al.   RESEARCH IN MICROBIOLOGY

En route to a genome-based classification of Archaea and Bacteria?

(2010) H.-P. Klenk et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

Phylogenetic Diversity and Metabolic Potential Revealed in a Glacier Ice Metagenome

(2009) C. Simon et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

Horizontal gene transfer of zinc and non-zinc forms of bacterial ribosomal protein S4

(2009) Ke Chen et al.   BMC EVOLUTIONARY BIOLOGY

Phylum Verrucomicrobia representatives share a compartmentalized cell plan with members of bacterial phylum Planctomycetes

(2009) Kuo-Chang Lee et al.   BMC MICROBIOLOGY

Focus:Synergistetes

(2009) Philip Hugenholtz et al.   ENVIRONMENTAL MICROBIOLOGY

Evaluation of the phylogenetic position of the sulfate-reducing bacterium Thermodesulfovibrio yellowstonii (phylum Nitrospirae) by means of gene order data from completely sequenced genomes

(2009) T. Kunisawa   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Further refinement of the phylogeny of the Halobacteriaceae based on the full-length RNA polymerase subunit B' (rpoB') gene

(2009) H. Minegishi et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Mapping the Tree of Life: Progress and Prospects

(2009) N. R. Pace   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea

(2009) Dongying Wu et al.   NATURE

MBGD update 2010: toward a comprehensive resource for exploring microbial genome diversity

(2009) Ikuo Uchiyama et al.   NUCLEIC ACIDS RESEARCH

eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations

(2009) J. Muller et al.   NUCLEIC ACIDS RESEARCH

On the chimeric nature, thermophilic origin, and phylogenetic placement of the Thermotogales

(2009) O. Zhaxybayeva et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phylogenomic analyses support the monophyly of Excavata and resolve relationships among eukaryotic "supergroups"

(2009) V. Hampl et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Network analyses structure genetic diversity in independent genetic worlds

(2009) S. Halary et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Accounting for horizontal gene transfers explains conflicting hypotheses regarding the position of aquificales in the phylogeny of Bacteria

(2008) Bastien Boussau et al.   BMC EVOLUTIONARY BIOLOGY

Sorting out the mix in microbial genomics

(2008) Michael Y. Galperin   ENVIRONMENTAL MICROBIOLOGY

Diversity of microbes associated with the marine sponge, Haliclona simulans, isolated from Irish waters and identification of polyketide synthase genes from the sponge metagenome

(2008) Jonathan Kennedy et al.   ENVIRONMENTAL MICROBIOLOGY

Reticulate Representation of Evolutionary and Functional Relationships between Phage Genomes

(2008) G. Lima-Mendez et al.   MOLECULAR BIOLOGY AND EVOLUTION

A Comparison of Phylogenetic Network Methods Using Computer Simulation

(2008) Steven M. Woolley et al.   PLoS One

FastBLAST: Homology Relationships for Millions of Proteins

(2008) Morgan N. Price et al.   PLoS One

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

The Impact of Reticulate Evolution on Genome Phylogeny

(2008) Robert G. Beiko et al.   SYSTEMATIC BIOLOGY

Testing Congruence in Phylogenomic Analysis

(2008) Jessica W. Leigh et al.   SYSTEMATIC BIOLOGY