Standardized benchmarking in the quest for orthologs

Quest for Orthologs Entails Quest for Tree of Life: In Search of the Gene Stream

(2015) Brigitte Boeckmann et al.   Genome Biology and Evolution

Tree of Life Reveals Clock-Like Speciation and Diversification

(2015) S. Blair Hedges et al.   MOLECULAR BIOLOGY AND EVOLUTION

Big data and other challenges in the quest for orthologs

(2014) E. L. L. Sonnhammer et al.   BIOINFORMATICS

OrthoInspector 2.0: Software and database updates

(2014) Benjamin Linard et al.   BIOINFORMATICS

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

InParanoid 8: orthology analysis between 273 proteomes, mostly eukaryotic

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

Bidirectional Best Hits Miss Many Orthologs in Duplication-Rich Clades such as Plants and Animals

(2013) Daniel A. Dalquen et al.   Genome Biology and Evolution

Hieranoid: Hierarchical Orthology Inference

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

Functional and evolutionary implications of gene orthology

(2013) Toni Gabaldón et al.   NATURE REVIEWS GENETICS

eggNOG v4.0: nested orthology inference across 3686 organisms

(2013) Sean Powell 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

TreeFam v9: a new website, more species and orthology-on-the-fly

(2013) Fabian Schreiber et al.   NUCLEIC ACIDS RESEARCH

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

Evolution of the Ferric Reductase Domain (FRD) Superfamily: Modularity, Functional Diversification, and Signature Motifs

(2013) Xuezhi Zhang et al.   PLoS One

Inferring Hierarchical Orthologous Groups from Orthologous Gene Pairs

(2013) Adrian M. Altenhoff et al.   PLoS One

Toward community standards in the quest for orthologs

(2012) C. Dessimoz et al.   BIOINFORMATICS

Roundup 2.0: enabling comparative genomics for over 1800 genomes

(2012) T. F. DeLuca et al.   BIOINFORMATICS

A Tight Link between Orthologs and Bidirectional Best Hits in Bacterial and Archaeal Genomes

(2012) Yuri I. Wolf et al.   Genome Biology and Evolution

PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees

(2012) Huaiyu Mi et al.   NUCLEIC ACIDS RESEARCH

On the Use of Gene Ontology Annotations to Assess Functional Similarity among Orthologs and Paralogs: A Short Report

(2012) Paul D. Thomas et al.   PLoS Computational Biology

The Ortholog Conjecture Is Untestable by the Current Gene Ontology but Is Supported by RNA Sequencing Data

(2012) Xiaoshu Chen et al.   PLoS Computational Biology

Resolving the Ortholog Conjecture: Orthologs Tend to Be Weakly, but Significantly, More Similar in Function than Paralogs

(2012) Adrian M. Altenhoff et al.   PLoS Computational Biology

Orthology prediction methods: A quality assessment using curated protein families

(2011) Kalliopi Trachana et al.   BIOESSAYS

OrthoInspector: comprehensive orthology analysis and visual exploration

(2011) Benjamin Linard et al.   BMC BIOINFORMATICS

Editorial: Orthology and applications

(2011) C. Dessimoz   BRIEFINGS IN BIOINFORMATICS

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

Reorganizing the protein space at the Universal Protein Resource (UniProt)

(2011)   NUCLEIC ACIDS RESEARCH

The UniProt-GO Annotation database in 2011

(2011) E. C. Dimmer et al.   NUCLEIC ACIDS RESEARCH

Evaluating Ortholog Prediction Algorithms in a Yeast Model Clade

(2011) Leonidas Salichos et al.   PLoS One

Testing the Ortholog Conjecture with Comparative Functional Genomic Data from Mammals

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

Parallelization of the MAFFT multiple sequence alignment program

(2010) Kazutaka Katoh et al.   BIOINFORMATICS

GIGA: a simple, efficient algorithm for gene tree inference in the genomic age

(2010) Paul D Thomas   BMC 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

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

Simultaneous Bayesian gene tree reconstruction and reconciliation analysis

(2009) O. Akerborg et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Probabilistic Orthology Analysis

(2009) Bengt Sennblad et al.   SYSTEMATIC BIOLOGY

Phylogenetic and Functional Assessment of Orthologs Inference Projects and Methods

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

Joining forces in the quest for orthologs

(2009) Toni Gabaldón et al.   GENOME BIOLOGY

Recent developments in the MAFFT multiple sequence alignment program

(2008) K. Katoh et al.   BRIEFINGS IN BIOINFORMATICS

EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates

(2008) A. J. Vilella et al.   GENOME RESEARCH