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

Endosymbiotic origin and differential loss of eukaryotic genes

(2015) Chuan Ku et al.   NATURE

Structure and function of the global ocean microbiome

(2015) S. Sunagawa et al.   SCIENCE

OrthoInspector 2.0: Software and database updates

(2014) Benjamin Linard et al.   BIOINFORMATICS

An integrated catalog of reference genes in the human gut microbiome

(2014) Junhua Li et al.   NATURE BIOTECHNOLOGY

Expanded microbial genome coverage and improved protein family annotation in the COG database

(2014) Michael Y. Galperin et al.   NUCLEIC ACIDS RESEARCH

OrthoDB v8: update of the hierarchical catalog of orthologs and the underlying free software

(2014) Evgenia V. Kriventseva et al.   NUCLEIC ACIDS RESEARCH

The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements

(2014) Adrian M. Altenhoff et al.   NUCLEIC ACIDS RESEARCH

Gene Ontology Consortium: going forward

(2014)   NUCLEIC ACIDS RESEARCH

SMART: recent updates, new developments and status in 2015

(2014) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2015

(2014) Fiona Cunningham et al.   NUCLEIC ACIDS RESEARCH

InParanoid 8: orthology analysis between 273 proteomes, mostly eukaryotic

(2014) Erik L.L. Sonnhammer et al.   NUCLEIC ACIDS RESEARCH

STRING v10: protein–protein interaction networks, integrated over the tree of life

(2014) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

UniProt: a hub for protein information

(2014)   NUCLEIC ACIDS RESEARCH

A Phylogeny-Based Benchmarking Test for Orthology Inference Reveals the Limitations of Function-Based Validation

(2014) Kalliopi Trachana et al.   PLoS One

Hieranoid: Hierarchical Orthology Inference

(2013) Fabian Schreiber et al.   JOURNAL OF MOLECULAR BIOLOGY

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

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

Functional and evolutionary implications of gene orthology

(2013) Toni Gabaldón et al.   NATURE REVIEWS GENETICS

SIMAP—the database of all-against-all protein sequence similarities and annotations with new interfaces and increased coverage

(2013) Roland Arnold et al.   NUCLEIC ACIDS RESEARCH

eggNOG v4.0: nested orthology inference across 3686 organisms

(2013) Sean Powell et al.   NUCLEIC ACIDS RESEARCH

Ensembl Genomes 2013: scaling up access to genome-wide data

(2013) Paul Julian Kersey et al.   NUCLEIC ACIDS RESEARCH

RefSeq microbial genomes database: new representation and annotation strategy

(2013) Tatiana Tatusova et al.   NUCLEIC ACIDS RESEARCH

PhylomeDB v4: zooming into the plurality of evolutionary histories of a genome

(2013) Jaime Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

The genome portal of the Department of Energy Joint Genome Institute: 2014 updates

(2013) Henrik Nordberg et al.   NUCLEIC ACIDS RESEARCH

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Data, information, knowledge and principle: back to metabolism in KEGG

(2013) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

STITCH 4: integration of protein–chemical interactions with user data

(2013) Michael Kuhn et al.   NUCLEIC ACIDS RESEARCH

Following Gene Duplication, Paralog Interference Constrains Transcriptional Circuit Evolution

(2013) Christopher R. Baker et al.   SCIENCE

Orthologous Gene Clusters and Taxon Signature Genes for Viruses of Prokaryotes

(2012) D. M. Kristensen et al.   JOURNAL OF BACTERIOLOGY

Orthology prediction methods: A quality assessment using curated protein families

(2011) Kalliopi Trachana et al.   BIOESSAYS

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

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

Testing the Ortholog Conjecture with Comparative Functional Genomic Data from Mammals

(2011) Nathan L. Nehrt et al.   PLoS Computational Biology

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Assigning duplication events to relative temporal scales in genome-wide studies

(2010) J. Huerta-Cepas et al.   BIOINFORMATICS

ETE: a python Environment for Tree Exploration

(2010) Jaime Huerta-Cepas et al.   BMC BIOINFORMATICS

MetaPhOrs: orthology and paralogy predictions from multiple phylogenetic evidence using a consistency-based confidence score

(2010) Leszek P. Pryszcz et al.   NUCLEIC ACIDS RESEARCH

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

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

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

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

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

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

How confident can we be that orthologs are similar, but paralogs differ?

(2009) Romain A. Studer et al.   TRENDS IN GENETICS