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Motivation: When gene duplication occurs, one of the copies may become free of selective pressure and evolve at an accelerated pace. This has important consequences on the prediction of orthology relationships, since two orthologous genes separated by divergence after duplication may differ in both sequence and function. In this work, we make the distinction between the primary orthologs, which have not been affected by accelerated mutation rates on their evolutionary path, and the secondarydoi:10.1093/bioinformatics/bty242 pmid:29950018 pmcid:PMC6022570 fatcat:abs2qab4rjcetbmiwnffm6w4py