Deep mitochondrial origin outside the sampled alphaproteobacteria

metaSPAdes: a new versatile metagenomic assembler

(2017) Sergey Nurk et al.   GENOME RESEARCH

ModelFinder: fast model selection for accurate phylogenetic estimates

(2017) Subha Kalyaanamoorthy et al.   NATURE METHODS

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

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

SAR202 Genomes from the Dark Ocean Predict Pathways for the Oxidation of Recalcitrant Dissolved Organic Matter

(2017) Zachary Landry et al.   mBio

Late acquisition of mitochondria by a host with chimaeric prokaryotic ancestry

(2016) Alexandros A. Pittis et al.   NATURE

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

Pathogen to powerhouse

(2016) S. G. Ball et al.   SCIENCE

Genome-Based Microbial Taxonomy Coming of Age

(2016) Philip Hugenholtz et al.   Cold Spring Harbor Perspectives in Biology

Single-cell genomics of a rare environmental alphaproteobacterium provides unique insights into Rickettsiaceae evolution

(2015) Joran Martijn et al.   ISME Journal

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

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

Structure and function of the global ocean microbiome

(2015) S. Sunagawa et al.   SCIENCE

Tara Oceans studies plankton at planetary scale

(2015) P. Bork et al.   SCIENCE

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

MitoCOGs: clusters of orthologous genes from mitochondria and implications for the evolution of eukaryotes

(2014) Sivakumar Kannan et al.   BMC EVOLUTIONARY BIOLOGY

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

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

Binning metagenomic contigs by coverage and composition

(2014) Johannes Alneberg et al.   NATURE METHODS

Phylogenomic Reconstruction Indicates Mitochondrial Ancestor Was an Energy Parasite

(2014) Zhang Wang et al.   PLoS One

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

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

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

Insights into the phylogeny and coding potential of microbial dark matter

(2013) Christian Rinke et al.   NATURE

New rRNA Gene-Based Phylogenies of the Alphaproteobacteria Provide Perspective on Major Groups, Mitochondrial Ancestry and Phylogenetic Instability

(2013) Matteo P. Ferla et al.   PLoS One

Comparative and Phylogenomic Evidence That the Alphaproteobacterium HIMB59 Is Not a Member of the Oceanic SAR11 Clade

(2013) Johan Viklund et al.   PLoS One

PhyloBayes MPI: Phylogenetic Reconstruction with Infinite Mixtures of Profiles in a Parallel Environment

(2013) Nicolas Lartillot et al.   SYSTEMATIC BIOLOGY

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

(2012) Y. Peng et al.   BIOINFORMATICS

The SAR11 Group of Alpha-Proteobacteria Is Not Related to the Origin of Mitochondria

(2012) Naiara Rodríguez-Ezpeleta et al.   PLoS One

Phylogenomic Evidence for the Presence of a Flagellum and cbb3 Oxidase in the Free-Living Mitochondrial Ancestor

(2011) D. Sassera et al.   MOLECULAR BIOLOGY AND EVOLUTION

Independent Genome Reduction and Phylogenetic Reclassification of the Oceanic SAR11 Clade

(2011) J. Viklund et al.   MOLECULAR BIOLOGY AND EVOLUTION

A Phylometagenomic Exploration of Oceanic Alphaproteobacteria Reveals Mitochondrial Relatives Unrelated to the SAR11 Clade

(2011) Björn Brindefalk et al.   PLoS One

Intracellular Rickettsiales: Insights into manipulators of eukaryotic cells

(2011) Aurélie Renvoisé et al.   TRENDS IN MOLECULAR MEDICINE

Phylogenomic evidence for a common ancestor of mitochondria and the SAR11 clade

(2011) J. Cameron Thrash et al.   Scientific Reports

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

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

Phylogeny of Gammaproteobacteria

(2010) K. P. Williams et al.   JOURNAL OF BACTERIOLOGY

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

Empirical profile mixture models for phylogenetic reconstruction

(2008) Le Si Quang et al.   BIOINFORMATICS