biostudies-literatureUnknown11(3)Weighill DAWe present and develop the theory of 3-way networks, a type of hypergraph in which each edge models relationships between triplets of objects as opposed to pairs of objects as done by standard network models. We explore approaches of how to prune these 3-way networks, illustrate their utility in comparative genomics and demonstrate how they find relationships which would be missed by standard 2-way network models using a phylogenomic dataset of 211 bacterial genomes.PLoS computational biologye1004079https://www.ebi.ac.uk/biostudies/studies/S-EPMC4376783biostudies-literature3-way networks: application of hypergraphs for modelling increased complexity in comparative genomics.PMC4376783Weighill DAJacobson DAfalse3-way networks: application of hypergraphs for modelling increased complexity in comparative genomics.We present and develop the theory of 3-way networks, a type of hypergraph in which each edge models relationships between triplets of objects as opposed to pairs of objects as done by standard network models. We explore approaches of how to prune these 3-way networks, illustrate their utility in comparative genomics and demonstrate how they find relationships which would be missed by standard 2-way network models using a phylogenomic dataset of 211 bacterial genomes.2015-01-01T00:00:00Z2015 Mar2025-04-19T00:47:44.508Z2019-03-26T22:40:04ZS-EPMC43767832581580210.1371/journal.pcbi.1004079