Genome-scale orthology assignments are usually based on reciprocal best matches. In the absence of horizontal gene transfer (HGT), every pair of orthologs forms a reciprocal best match. Incorrect orthology assignments therefore are always false positives in the reciprocal best match graph. We consider duplication/loss scenarios and characterize unambiguous false-positive (u-fp) orthology assignments, that is, edges in the best match graphs (BMGs) that cannot correspond to orthologs for any gene tree that explains the BMG. Moreover, we provide a polynomial-time algorithm to identify all u-fp orthology assignments in a BMG. Simulations show that at least \(75\%\) of all incorrect orthology assignments can be detected in this manner. All results rely only on the structure of the BMGs and not on any a priori knowledge about underlying gene or species trees.

基因组规模的直系同源分配通常基于相互的最佳匹配。在没有水平基因转移（HGT）的情况下，每对直系同源物形成相互的最佳匹配。因此，不正确的直系同源分配在倒数最佳匹配图中始终是误报。我们考虑重复/丢失场景，并描述明确的假阳性（ u-fp ）直系同源分配，即最佳匹配图（BMG）中的边不能对应于解释 BMG 的任何基因树的直向同源物。此外，我们提供了一种多项式时间算法来识别 BMG 中的所有u-fp直系同源分配。模拟表明，至少\(75\%\)的所有不正确的同源分配可以通过这种方式被检测到。所有结果仅依赖于 BMG 的结构，而不依赖于任何有关潜在基因或物种树的先验知识。