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

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

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

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

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

ALF—A Simulation Framework for Genome Evolution

(2011) Daniel A. Dalquen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evaluating Ortholog Prediction Algorithms in a Yeast Model Clade

(2011) Leonidas Salichos et al.   PLoS One

OMA 2011: orthology inference among 1000 complete genomes

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

InParanoid 7: new algorithms and tools for eukaryotic orthology analysis

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

Phylogenetic and Functional Assessment of Orthologs Inference Projects and Methods

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