Supporting files for the analyses within "Begomovirus species demarcation based on genome-seqeunce identity often yields non-monophyletic species: A case study of sweet potato-infecting begomoviruses." 398 full-length genomes from NCBI GenBank (accession numbers given in all of analysis files) were used for all analyses. This includes phylogenetic analysis (aligment in fasta format, maximum likelihood tree in nexus format, with support in aLRT/UF boot), percent nucleotide identity analysis (sequence demarcation tool format), recombination analysis (recombination detection program format, excel spreadsheets analysing the resulting events) and network analysis (four files in cytoscape format).