Campos LRS, Trefflich S, Morais DAA, Imparato DO, Chagas VS, Albanus RD, Dalmolin RJS, Castro MAA. Bridge: A New Algorithm for Rooting Orthologous Genes in Large-Scale Evolutionary Analyses.
Mol Biol Evol 2024;
41:msae019. [PMID:
38306290 PMCID:
PMC10873778 DOI:
10.1093/molbev/msae019]
[Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 01/21/2024] [Accepted: 01/29/2024] [Indexed: 02/04/2024] Open
Abstract
Orthology information has been used for searching patterns in high-dimensional data, allowing transferring functional information between species. The key concept behind this strategy is that orthologous genes share ancestry to some extent. While reconstructing the history of a single gene is feasible with the existing computational resources, the reconstruction of entire biological systems remains challenging. In this study, we present Bridge, a new algorithm designed to infer the evolutionary root of orthologous genes in large-scale evolutionary analyses. The Bridge algorithm infers the evolutionary root of a given gene based on the distribution of its orthologs in a species tree. The Bridge algorithm is implemented in R and can be used either to assess genetic changes across the evolutionary history of orthologous groups or to infer the onset of specific traits in a biological system.
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