{"about":{"site":"https://codewithpapers.app","non_affiliation":"Code with Papers and Syntology are not affiliated with, endorsed by, or sponsored by Papers with Code, Meta, or the pwc-archive mirror.","licence":"CC BY-SA 4.0","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","attribution":"https://codewithpapers.app/attribution","modified":"archive material modified by Syntology; see the attribution page"},"url":"/paper/best-match-graphs","title":"Best Match Graphs","arxiv_id":"1803.10989","date":"2018-03-29","proceeding":null,"authors":["Manuela Geiß","Edgar Chavez","Marcos Gonzalez","Alitzel Lopez","Bärbel M. R. Stadler","Dulce I. Valdivia","Marc Hellmuth","Maribel H. Rosales","Peter F. Stadler"],"abstract":"THIS IS A CORRECTED VERSION INCLUDING AN APPENDED CORRIGENDUM. Best match graphs arise naturally as the first processing intermediate in algorithms for orthology detection. Let $T$ be a phylogenetic (gene) tree $T$ and $\\sigma$ an assignment of leaves of $T$ to species. The best match graph $(G,\\sigma)$ is a digraph that contains an arc from $x$ to $y$ if the genes $x$ and $y$ reside in different species and $y$ is one of possibly many (evolutionary) closest relatives of $x$ compared to all other genes contained in the species $\\sigma(y)$. Here, we characterize best match graphs and show that it can be decided in cubic time and quadratic space whether $(G,\\sigma)$ derived from a tree in this manner. If the answer is affirmative, there is a unique least resolved tree that explains $(G,\\sigma)$, which can also be constructed in cubic time.","url_abs":"https://arxiv.org/abs/1803.10989v4","url_pdf":"https://arxiv.org/pdf/1803.10989v4.pdf","source":{"archive":"pwc-archive (Hugging Face), CC BY-SA 4.0","snapshot":"2025-07-28","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","row_kind":"links_only","authors_date_abstract":"arXiv metadata, CC0 1.0 (https://info.arxiv.org/help/license), from the Kaggle arXiv metadata snapshot of 2026-09-12"},"code_links":[{"paper_slug":"best-match-graphs","repo_url":"https://github.com/nilavanilla/best-match-graphs","is_official":0,"mentioned_in_paper":0,"mentioned_in_github":1,"framework":"none","reach":null}],"tasks":[],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"syntology_url":null,"atlas_url":null,"mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}