Begomovirus DNA-A and DNA-B Recombination: Curated Alignments, HyPhy GARD Analyses, and RDP4-Validated Events

This dataset supports the recombination analysis of begomovirus genome segments (DNA-A and DNA-B). It contains curated sequence inputs, multiple sequence alignments, HyPhy GARD outputs, and a validation table based on RDP4 that harmonizes events across both segments. The dataset is designed for full reproducibility and secondary reuse. Contents Sequences and Alignments : Raw FASTA inputs; deduplicated sets (SeqKit v2.1.0); MAFFT v7.505 alignments; and masked alignments (gap-rich columns >50% removed, and IUPAC ambiguities retained as bases). Redundancy Reduction: CD-HIT-EST v4.8.1 centroid sets at 99% identity and their realignments. HyPhy GARD (v2.5.70): JSON outputs and best-fit snapshots for centroid scans (GTR+G, four classes; --mode Faster; --max-breakpoints 8–12), and where AICc permitted, full realignments (HKY+G, two classes; --mode Normal; --max-breakpoints 8). RDP4 validation exports ("Breakpoint positions/Detection methods") and a harmonized table (dnaA+dnaB) of validated events with the following fields: event_id, segment, recombinant, major_parent, minor_parent, begin, end, n_sig_methods, and sig_methods. The validation criterion is ≥3 methods (RDP, GENECONV, BootScan, MaxChi, Chimaera, SiScan, and 3Seq, as well as PhylPro/LARD, if present) with p < 0.05 or non-NS indicators in the export.