OrthoMCL is a genome-scale algorithm for grouping orthologous protein sequences. It provides not only groups shared by two or more species/genomes, but also groups representing species-specific gene expansion families. So it serves as an important utility for automated eukaryotic genome annotation. OrthoMCL starts with reciprocal best hits within each genome as potential in-paralog/recent paralog pairs and reciprocal best hits across any two genomes as potential ortholog pairs. Related proteins are interlinked in a similarity graph.
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Li Li, Christian J. Stoeckert, Jr., and David S. Roos
OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes
Genome Res. 2003 13: 2178-2189