Orthology prediction methods: A quality assessment using curated protein families

Computational methods for Gene Orthology inference

(2011) D. M. Kristensen et al.   BRIEFINGS IN BIOINFORMATICS

Evaluating Ortholog Prediction Algorithms in a Yeast Model Clade

(2011) Leonidas Salichos et al.   PLoS One

The dynamic genome of Hydra

(2010) Jarrod A. Chapman et al.   NATURE

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

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

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

Ensembl 2011

(2010) P. Flicek et al.   NUCLEIC ACIDS RESEARCH

OrthoDB: the hierarchical catalog of eukaryotic orthologs in 2011

(2010) Robert M. Waterhouse et al.   NUCLEIC ACIDS RESEARCH

OMA 2011: orthology inference among 1000 complete genomes

(2010) A. M. Altenhoff 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

2× genomes - depth does matter

(2010) Michel C Milinkovitch et al.   GENOME BIOLOGY

AQUA: automated quality improvement for multiple sequence alignments

(2009) J. Muller 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

InParanoid 7: new algorithms and tools for eukaryotic orthology analysis

(2009) G. Ostlund et al.   NUCLEIC ACIDS RESEARCH

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

Phylogenetic and Functional Assessment of Orthologs Inference Projects and Methods

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

The Origins of Multicellularity and the Early History of the Genetic Toolkit For Animal Development

(2008) Antonis Rokas   Annual Review of Genetics

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

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

Discovering Functional Novelty in Metagenomes: Examples from Light-Mediated Processes

(2008) A. H. Singh et al.   JOURNAL OF BACTERIOLOGY

The Trichoplax genome and the nature of placozoans

(2008) Mansi Srivastava et al.   NATURE

The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans

(2008) Nicole King et al.   NATURE

The quest for orthologs: finding the corresponding gene across genomes

(2008) Arnold Kuzniar et al.   TRENDS IN GENETICS

Large-scale assignment of orthology: back to phylogenetics?

(2008) Toni Gabaldón   GENOME BIOLOGY

Domain Tree-Based Analysis of Protein Architecture Evolution

(2007) K. Forslund et al.   MOLECULAR BIOLOGY AND EVOLUTION