eggNOG v4.0: nested orthology inference across 3686 organisms

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

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

Metagenomic species profiling using universal phylogenetic marker genes

(2013) Shinichi Sunagawa et al.   NATURE METHODS

Accurate and universal delineation of prokaryotic species

(2013) Daniel R Mende et al.   NATURE METHODS

Functional and evolutionary implications of gene orthology

(2013) Toni Gabaldón et al.   NATURE REVIEWS GENETICS

The Impact of Gene Duplication, Insertion, Deletion, Lateral Gene Transfer and Sequencing Error on Orthology Inference: A Simulation Study

(2013) Daniel A. Dalquen et al.   PLoS One

Updated clusters of orthologous genes for Archaea: a complex ancestor of the Archaea and the byways of horizontal gene transfer

(2012) Yuri I Wolf et al.   Biology Direct

Genomic variation landscape of the human gut microbiome

(2012) Siegfried Schloissnig et al.   NATURE

KEGG OC: a large-scale automatic construction of taxonomy-based ortholog clusters

(2012) Akihiro Nakaya et al.   NUCLEIC ACIDS RESEARCH

Update on activities at the Universal Protein Resource (UniProt) in 2013

(2012)   NUCLEIC ACIDS RESEARCH

New Approaches for Isolation of Previously Uncultivated Oral Bacteria

(2011) M. V. Sizova et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Orthology prediction methods: A quality assessment using curated protein families

(2011) Kalliopi Trachana et al.   BIOESSAYS

Conceptual framework and pilot study to benchmark phylogenomic databases based on reference gene trees

(2011) B. Boeckmann et al.   BRIEFINGS IN BIOINFORMATICS

Letter to the Editor: SeqXML and OrthoXML: standards for sequence and orthology information

(2011) T. Schmitt et al.   BRIEFINGS IN BIOINFORMATICS

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

(2011) F. Sievers et al.   Molecular Systems Biology

eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges

(2011) S. Powell et al.   NUCLEIC ACIDS RESEARCH

SMART 7: recent updates to the protein domain annotation resource

(2011) I. Letunic et al.   NUCLEIC ACIDS RESEARCH

Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy

(2011) I. Letunic et al.   NUCLEIC ACIDS RESEARCH

The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools

(2011) Philippe Lamesch et al.   NUCLEIC ACIDS RESEARCH

NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy

(2011) K. D. Pruitt et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2012

(2011) P. Flicek et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database

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

Dissecting Plant Genomes with the PLAZA Comparative Genomics Platform

(2011) M. Van Bel et al.   PLANT PHYSIOLOGY

Evaluating Ortholog Prediction Algorithms in a Yeast Model Clade

(2011) Leonidas Salichos et al.   PLoS One

Identifying Single Copy Orthologs in Metazoa

(2011) Christopher J. Creevey et al.   PLoS Computational Biology

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Identification of shared single copy nuclear genes in Arabidopsis, Populus, Vitis and Oryza and their phylogenetic utility across various taxonomic levels

(2010) Jill M Duarte et al.   BMC EVOLUTIONARY BIOLOGY

MLTreeMap - accurate Maximum Likelihood placement of environmental DNA sequences into taxonomic and functional reference phylogenies

(2010) Manuel Stark et al.   BMC GENOMICS

Limitations of next-generation genome sequence assembly

(2010) Can Alkan et al.   NATURE METHODS

PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions

(2010) J. Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored

(2010) D. Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

OMA 2011: orthology inference among 1000 complete genomes

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

2× genomes - depth does matter

(2010) Michel C Milinkovitch et al.   GENOME BIOLOGY

Benchmarking homology detection procedures with low complexity filters

(2009) Kristoffer Forslund et al.   BIOINFORMATICS

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

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

Jalview Version 2--a multiple sequence alignment editor and analysis workbench

(2009) A. M. Waterhouse et al.   BIOINFORMATICS

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

SIMAP—a comprehensive database of pre-calculated protein sequence similarities, domains, annotations and clusters

(2009) Thomas Rattei et al.   NUCLEIC ACIDS RESEARCH

Phylogenetic and Functional Assessment of Orthologs Inference Projects and Methods

(2009) Adrian M. Altenhoff et al.   PLoS Computational Biology

Database resources of the National Center for Biotechnology Information

(2008) E. W. Sayers et al.   NUCLEIC ACIDS RESEARCH

GiardiaDB and TrichDB: integrated genomic resources for the eukaryotic protist pathogens Giardia lamblia and Trichomonas vaginalis

(2008) C. Aurrecoechea et al.   NUCLEIC ACIDS RESEARCH

GenBank

(2008) D. A. Benson et al.   NUCLEIC ACIDS RESEARCH