orthology

Orthology, paralogy and proposed classification for paralog subtypes
OMA 2011: orthology inference among 1000 complete genomes.
eggNOG v4.0: nested orthology inference across 3686 organisms
Assessing performance of orthology detection strategies applied to eukaryotic genomes
SOrt-ITEMS: Sequence orthology based approach for improved taxonomic estimation of metagenomic sequences
InParanoid 7: new algorithms and tools for eukaryotic orthology analysis.
Comparison of the Complete Protein Sets of Worm and Yeast: Orthology and Divergence
Automated ortholog inference from phylogenetic trees and calculation of orthology reliability.
Automated genome annotation and pathway identification using the KEGG Orthology (KO) as a controlled vocabulary.
Global alignment of multiple protein interaction networks with application to functional orthology detection.