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arXiv · 2609.21700

Best Matches in Phylogenetic Networks

Patricia A. Ebert·Peter F. Stadler·Marc Hellmuth
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Abstract

Best match graphs (BMGs) were introduced in mathematical phylogenetics to describe the concept of closest relatives for related genes (leaves of rooted tree) in different organisms (defining leaf colors). We generalize this concept here to leaf-colored rooted networks, where least common ancestors are in general neither unique nor comparable. We characterize BMGs of rooted networks as those vertex-colored digraphs that are properly colored and satisfy an easy-to-check condition that we call the sicor-in-hub property. BMGs can be recognized in linear time and an explaining network can be constructed in quadratic time. Analogous results are obtained for reciprocal best match graphs (RBMGs), where an edge $\{x,y\}$ corresponds to pairs of vertices with different color that are mutually closest relatives.

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Patricia A. Ebert, Peter F. Stadler, Marc Hellmuth. 2026-09-18. Best Matches in Phylogenetic Networks. https://arxiv.org/abs/2609.21700

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