Ramos González, MarcosRamos González, VíctorArvanitidou, ChristinaHernández García, JorgeGarcía González, MercedesRomero Campero, Francisco José2025-03-282025-03-282023Ramos González, M., Ramos González, V., Arvanitidou, C., Hernández García, J., García González, M. y Romero Campero, F.J. (2023). PharaohFUN: PHylogenomic Analysis foR plAnt prOtein History and FUNction elucidation. https://doi.org/10.1101/2023.08.01.551440.https://hdl.handle.net/11441/170976Motivation Since DNA sequencing has turned commonplace, the development of efficient methods and tools to explore gene sequences has become indispensable. In particular, despite photosynthetic eukaryotes constituting the largest percentage of terrestrial biomass, computational functional characterization of gene sequences in these organisms still predominantly relies on comparisons with Arabidopsis thaliana and other angiosperms. This paper introduces PharaohFUN, a web application designed for the evolutionary and functional analysis of protein sequences in photosynthetic eukaryotes, leveraging orthology relationships between them. Results PharaohFUN incorporates a homogeneous representative sampling of key species in this group, bridging clades that have traditionally been studied separately, thus establishing a comprehensive evolutionary framework to draw conclusions about sequence evolution and function. For this purpose, it incorporates modules for exploring gene tree evolutionary history, domain identification, multiple sequence alignments, and functional annotation. The study of the CCA1 protein exemplifies how PharaohFUN unifies results for both land plants and chlorophyte microalgae, accurately tracing the evolutionary history of this protein.application/pdf23 p.engAttribution-NonCommercial-NoDerivatives 4.0 Internationalhttp://creativecommons.org/licenses/by-nc-nd/4.0/info:eu-repo/semantics/articleinfo:eu-repo/semantics/openAccesshttps://doi.org/10.1101/2023.08.01.551440