ezTree: an automated pipeline for identifying phylogenetic marker genes and inferring evolutionary relationships among uncultivated prokaryotic draft genomes

Fast and simple protein-alignment-guided assembly of orthologous gene families from microbiome sequencing reads

(2017) Daniel H. Huson et al.   Microbiome

Methanogenic paraffin degradation proceeds via alkane addition to fumarate by ‘Smithella’ spp. mediated by a syntrophic coupling with hydrogenotrophic methanogens

(2016) Boris Wawrik et al.   ENVIRONMENTAL MICROBIOLOGY

Chasing the elusive Euryarchaeota class WSA2: genomes reveal a uniquely fastidious methyl-reducing methanogen

(2016) Masaru Konishi Nobu et al.   ISME Journal

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets

(2016) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

Metagenomic Insights into the Uncultured Diversity and Physiology of Microbes in Four Hypersaline Soda Lake Brines

(2016) Charlotte D. Vavourakis et al.   Frontiers in Microbiology

A new view of the tree of life

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

Accurate binning of metagenomic contigs via automated clustering sequences using information of genomic signatures and marker genes

(2016) Hsin-Hung Lin et al.   Scientific Reports

Single-Cell-Genomics-Facilitated Read Binning of Candidate Phylum EM19 Genomes from Geothermal Spring Metagenomes

(2015) Eric D. Becraft et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Identification and Resolution of Microdiversity through Metagenomic Sequencing of Parallel Consortia

(2015) William C. Nelson et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Chloroflexi CL500-11 Populations That Predominate Deep-Lake Hypolimnion Bacterioplankton Rely on Nitrogen-Rich Dissolved Organic Matter Metabolism and C1Compound Oxidation

(2015) Vincent J. Denef et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets

(2015) Yu-Wei Wu et al.   BIOINFORMATICS

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

(2015) Dinghua Li et al.   BIOINFORMATICS

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

(2015) Donovan H. Parks et al.   GENOME RESEARCH

Refining the phylum Chlorobi by resolving the phylogeny and metabolic potential of the representative of a deeply branching, uncultivated lineage

(2015) Jennifer Hiras et al.   ISME Journal

Auxotrophy and intrapopulation complementary in the ‘interactome’ of a cultivated freshwater model community

(2015) Sarahi L. Garcia et al.   MOLECULAR ECOLOGY

Multi-omics of permafrost, active layer and thermokarst bog soil microbiomes

(2015) Jenni Hultman et al.   NATURE

The Pfam protein families database: towards a more sustainable future

(2015) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Methane metabolism in the archaeal phylum Bathyarchaeota revealed by genome-centric metagenomics

(2015) P. N. Evans et al.   SCIENCE

VizBin - an application for reference-independent visualization and human-augmented binning of metagenomic data

(2015) Cedric C Laczny et al.   Microbiome

Metagenomic Evidence for the Presence of Comammox Nitrospira -Like Bacteria in a Drinking Water System

(2015) Ameet J. Pinto et al.   mSphere

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes

(2014) M. Kim et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

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

GroopM: an automated tool for the recovery of population genomes from related metagenomes

(2014) Michael Imelfort et al.   PeerJ

MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm

(2014) Yu-Wei Wu et al.   Microbiome

Genome sequence-based species delimitation with confidence intervals and improved distance functions

(2013) Jan P Meier-Kolthoff et al.   BMC BIOINFORMATICS

Insights into the phylogeny and coding potential of microbial dark matter

(2013) Christian Rinke et al.   NATURE

Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes

(2013) Mads Albertsen et al.   NATURE BIOTECHNOLOGY

Systematic Identification of Gene Families for Use as “Markers” for Phylogenetic and Phylogeny-Driven Ecological Studies of Bacteria and Archaea and Their Major Subgroups

(2013) Dongying Wu et al.   PLoS One

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

The Binning of Metagenomic Contigs for Microbial Physiology of Mixed Cultures

(2012) Marc Strous et al.   Frontiers in Microbiology

Ray Meta: scalable de novo metagenome assembly and profiling

(2012) Sébastien Boisvert et al.   GENOME BIOLOGY

Meta-IDBA: a de Novo assembler for metagenomic data

(2011) Y. Peng et al.   BIOINFORMATICS

Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage

(2011) Chris L Dupont et al.   ISME Journal

EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data

(2011) Christopher S Miller et al.   GENOME BIOLOGY

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

FragGeneScan: predicting genes in short and error-prone reads

(2010) Mina Rho et al.   NUCLEIC ACIDS RESEARCH

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix

(2009) M. N. Price et al.   MOLECULAR BIOLOGY AND EVOLUTION

A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea

(2009) Dongying Wu et al.   NATURE

Shifting the genomic gold standard for the prokaryotic species definition

(2009) Michael Richter et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA