A rooted phylogeny resolves early bacterial evolution

One or two membranes? Diderm Firmicutes challenge the Gram‐positive/Gram‐negative divide

(2020) Daniela Megrian et al.   MOLECULAR MICROBIOLOGY

The reductive glycine pathway allows autotrophic growth of Desulfovibrio desulfuricans

(2020) Irene Sánchez-Andrea et al.   Nature Communications

Ancestral Absence of Electron Transport Chains in Patescibacteria and DPANN

(2020) Jacob P. Beam et al.   Frontiers in Microbiology

Genome-wide analysis of the Firmicutes illuminates the diderm/monoderm transition

(2020) Najwa Taib et al.   Nature Ecology & Evolution

Inference of Ancient Whole-Genome Duplications and the Evolution of Gene Duplication and Loss Rates

(2019) Arthur Zwaenepoel et al.   MOLECULAR BIOLOGY AND EVOLUTION

Origin of viruses: primordial replicators recruiting capsids from hosts

(2019) Mart Krupovic et al.   NATURE REVIEWS MICROBIOLOGY

Origins and evolution of CRISPR-Cas systems

(2019) Eugene V. Koonin et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Zombi: A phylogenetic simulator of trees, genomes and sequences that accounts for dead linages

(2019) Adrián A Davín et al.   BIOINFORMATICS

KofamKOALA: KEGG ortholog assignment based on profile HMM and adaptive score threshold

(2019) Takuya Aramaki et al.   BIOINFORMATICS

The distinction of CPR bacteria from other bacteria based on protein family content

(2019) Raphaël Méheust et al.   Nature Communications

Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea

(2019) Qiyun Zhu et al.   Nature Communications

Major New Microbial Groups Expand Diversity and Alter our Understanding of the Tree of Life

(2018) Cindy J. Castelle et al.   CELL

Evolutionary history of carbon monoxide dehydrogenase/acetyl-CoA synthase, one of the oldest enzymatic complexes

(2018) Panagiotis S. Adam et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A primordial and reversible TCA cycle in a facultatively chemolithoautotrophic thermophile

(2018) Takuro Nunoura et al.   SCIENCE

Gene transfers can date the tree of life

(2018) Adrián A. Davín et al.   Nature Ecology & Evolution

A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life

(2018) Donovan H Parks et al.   NATURE BIOTECHNOLOGY

Biosynthetic capacity, metabolic variety and unusual biology in the CPR and DPANN radiations

(2018) Cindy J. Castelle et al.   NATURE REVIEWS MICROBIOLOGY

eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses

(2018) Jaime Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper

(2017) Jaime Huerta-Cepas et al.   MOLECULAR BIOLOGY AND EVOLUTION

STRIDE: Species Tree Root Inference from Gene Duplication Events

(2017) David M Emms et al.   MOLECULAR BIOLOGY AND EVOLUTION

1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life

(2017) Supratim Mukherjee et al.   NATURE BIOTECHNOLOGY

Integrative modeling of gene and genome evolution roots the archaeal tree of life

(2017) Tom A. Williams et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Modeling Site Heterogeneity with Posterior Mean Site Frequency Profiles Accelerates Accurate Phylogenomic Estimation

(2017) Huai-Chun Wang et al.   SYSTEMATIC BIOLOGY

Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life

(2017) Donovan H. Parks et al.   Nature Microbiology

One step beyond a ribosome: The ancient anaerobic core

(2016) Filipa L. Sousa et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

Methanogenesis and the Wood–Ljungdahl Pathway: An Ancient, Versatile, and Fragile Association

(2016) Guillaume Borrel et al.   Genome Biology and Evolution

Sporulation, bacterial cell envelopes and the origin of life

(2016) Elitza I. Tocheva et al.   NATURE REVIEWS MICROBIOLOGY

Phylogenomic analysis supports the ancestral presence of LPS-outer membranes in the Firmicutes

(2016) Luisa CS Antunes et al.   eLife

The physiology and habitat of the last universal common ancestor

(2016) Madeline C. Weiss et al.   Nature Microbiology

A new view of the tree of life

(2016) Laura A. Hug et al.   Nature Microbiology

Genomic Expansion of Domain Archaea Highlights Roles for Organisms from New Phyla in Anaerobic Carbon Cycling

(2015) Cindy J. Castelle et al.   CURRENT BIOLOGY

Unusual biology across a group comprising more than 15% of domain Bacteria

(2015) Christopher T. Brown et al.   NATURE

An updated evolutionary classification of CRISPR–Cas systems

(2015) Kira S. Makarova et al.   NATURE REVIEWS MICROBIOLOGY

eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences

(2015) Jaime Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

Rooting the tree of life: the phylogenetic jury is still out

(2015) Richard Gouy et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The two-domain tree of life is linked to a new root for the Archaea

(2015) Kasie Raymann et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The origins of cellular life

(2014) Eugene V. Koonin   ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY

Biochemical fossils of the ancient transition from geoenergetics to bioenergetics in prokaryotic one carbon compound metabolism

(2014) Filipa L. Sousa et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Autotrophy at the thermodynamic limit of life: a model for energy conservation in acetogenic bacteria

(2014) Kai Schuchmann et al.   NATURE REVIEWS MICROBIOLOGY

Cas1–Cas2 complex formation mediates spacer acquisition during CRISPR–Cas adaptive immunity

(2014) James K Nuñez et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Gene similarity networks provide tools for understanding eukaryote origins and evolution

(2013) D. Alvarez-Ponce et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Lateral Gene Transfer from the Dead

(2013) Gergely J. Szöllősi et al.   SYSTEMATIC BIOLOGY

Efficient Exploration of the Space of Reconciled Gene Trees

(2013) Gergely J. Szöllősi et al.   SYSTEMATIC BIOLOGY

Phylogenetic modeling of lateral gene transfer reconstructs the pattern and relative timing of speciations

(2012) G. J. Szollosi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Turning the Crown Upside Down: Gene Tree Parsimony Roots the Eukaryotic Tree of Life

(2012) Laura A. Katz et al.   SYSTEMATIC BIOLOGY

Evolution and classification of the CRISPR–Cas systems

(2011) Kira S. Makarova et al.   NATURE REVIEWS MICROBIOLOGY

HMMER web server: interactive sequence similarity searching

(2011) R. D. Finn et al.   NUCLEIC ACIDS RESEARCH

Alternative Pathways of Carbon Dioxide Fixation: Insights into the Early Evolution of Life?

(2010) Georg Fuchs   Annual Review of Microbiology

BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments

(2010) Alexis Criscuolo et al.   BMC EVOLUTIONARY BIOLOGY

The Tree and Net Components of Prokaryote Evolution

(2010) Pere Puigbò et al.   Genome Biology and Evolution

Rapid evolutionary innovation during an Archaean genetic expansion

(2010) Lawrence A. David et al.   NATURE

Evidence for an early prokaryotic endosymbiosis

(2009) James A. Lake   NATURE

Genome beginnings: rooting the tree of life

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

Algorithm of OMA for large-scale orthology inference

(2008) Alexander CJ Roth et al.   BMC BIOINFORMATICS

A Major Clade of Prokaryotes with Ancient Adaptations to Life on Land

(2008) F. U. Battistuzzi et al.   MOLECULAR BIOLOGY AND EVOLUTION

An Improved General Amino Acid Replacement Matrix

(2008) S. Q. Le et al.   MOLECULAR BIOLOGY AND EVOLUTION