Underlying data for "Mapping glycoprotein structure reveals defining events in the evolution of the Flaviviridae"

This repository houses the underlying data for the study "Mapping glycoprotein structure reveals defining events in the evolution of the Flaviviridae", authored by Jonathon C.O. Mifsud, Spyros Lytras, Michael R. Oliver, Kamilla Toon, Vincenzo A. Costa, Edward C. Holmes, and Joe Grove. The dataset is organised into several directories: - alignments: Contains all alignment files, both trimmed and untrimmed, for NS5b and T2RNase trees. These include variations of alignments using different parameters and methods. - reference structures: Contains all structures used as references in FoldSeek analysis. - sequences: Holds sequence files including full genome sequences of Flaviviridae in .fasta formats, novel sequences identified in our study, and protein sequences extracted for alignment purposes. - structure guided glycoprotein phylogenies: Contains FoldSeek derived alignments and corresponding trees for E, E1 and E2 glycoproteins. The reference structures used for alignment are stated in the file names. - structures: Contains the Flaviviridae structures generated by AlphaFold and ESMFold. Structures are organised by taxa and numbered based on their block number. Polyprotein sequences were broken into 300 residue blocks, each overlapping by 100 residues. Numbering starts at Block_0 (residues 1-300) and continue sequentially (e.g. Block_1 = residues 100-400, Block_2 = residues 200-500, ...). - tables: Provides metadata tables, including domain annotations, RNase T2 analyses summaries, and novel viruses identified through data mining. - trees: Contains phylogenetic trees and analyses specific to NS5B protein and T2RNase protein, including all tree variations and consensus trees from TreeSpace analysis. For any queries, please contact the corresponding author at [e-mail] Original code and scripts related to the phylogenetic analyses are available at https://github.com/JonathonMifsud/Mapping-glycoprotein-structure-reveals-defining-events-in-the-evolution-of-the-Flaviviridae