Year: 2019
Type: article
Abstract: Best match graphs arise naturally as the first processing intermediate in algorithms for orthology detection. Let T be a phylogenetic (gene) tree T and [Formula: see text] an assignment of leaves of T to species. The best match graph [Formula: see text] 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 [Formula: see text]. Here, we characterize best match graphs and show that it can be decided in cubic time and quadratic space whether [Formula: see text] derived from a tree in this manner. If the answer is affirmative, there is a unique least resolved tree that explains [Formula: see text], which can also be constructed in cubic time.
Source: Journal of Mathematical Biology
Authors: Manuela Geiß, Edgar Chávez, Marcos González Laffitte, Alitzel López Sánchez, Bärbel M. R. Stadler, Dulce I. Valdivia, Marc Hellmuth, Maribel Hernández Rosales, Peter F. Stadler
Institutions: Leipzig University, Secretaría de Ciencia, Humanidades, Tecnología e Innovación, Universidad Nacional Autónoma de México, Max Planck Institute for Mathematics in the Sciences, Autonomous University of Aguascalientes, Universität Greifswald, Saarland University, University of Vienna, Santa Fe Institute, German Centre for Integrative Biodiversity Research, Universidad Nacional de Colombia
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: hybrid
Estimated APC paid: $2,690
Funders: Deutscher Akademischer Austauschdienst, Bundesministerium für Bildung und Forschung, Consejo Nacional de Ciencia y Tecnología, Bundesministerium für Wissenschaft, Forschung und Wirtschaft, Max-Planck-Gesellschaft, Fondo de Cooperación Internacional en Ciencia y Tecnología, German Network for Bioinformatics Infrastructure
OpenAlex ID: W2794905278