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Orthology and paralogy relations are often inferred by methods based on gene similarity, which usually yield a graph depicting the relationships between gene pairs. Such relation graphs are known to frequently contain errors, as they cannot be explained via a gene tree that both contains the depicted orthologs/paralogs, and that is consistent with a species tree S. This idea of detecting errors through inconsistency with a species tree has mostly been studied in the presence of speciation andarXiv:1705.01240v6 fatcat:iec4qm5zc5hclmyijvu6lkjlue