A wide variety of problems in computational biology, most notably the assessment of orthology, are solved with the help of reciprocal best matches. Using an evolutionary definition of best matches that captures the intuition behind the concept we clarify rigorously the relationships between reciprocal best matches, orthology, and evolutionary events under the assumption of duplication/loss scenarios. We show that the orthology graph is a subgraph of the reciprocal best match graph (RBMG). We furthermore give conditions under which an RBMG that is a cograph identifies the correct orthlogy relation. Using computer simulations we find that most false positive orthology assignments can be identified as so-called good quartets-and thus corrected-in the absence of horizontal transfer. Horizontal transfer, however, may introduce also false-negative orthology assignments.

中文翻译：

---

基因树与物种树的最佳匹配图和协调。


计算生物学中的各种问题，尤其是直系同源的评估，都是在相互最佳匹配的帮助下解决的。使用最佳匹配的进化定义来捕捉概念背后的直觉，我们在重复/丢失场景的假设下严格阐明了相互最佳匹配、同源性和进化事件之间的关系。我们证明直系图是倒数最佳匹配图（RBMG）的子图。我们还给出了作为 cograph 的 RBMG 识别正确的同源关系的条件。使用计算机模拟，我们发现大多数误报直系同源分配可以在没有水平转移的情况下被识别为所谓的良好四重奏，从而得到纠正。然而，水平转移也可能引入假阴性直系同源分配。