Evidence for recombination in dengue virus genomes

Appendix A — Supplementary Digital Materials These materials contain the supplementary digital materials for the manuscript "Evidence for recombination in dengue virus genomes," written by Hugo de Paula Oliveira (ORCiD: 0000-0001-5842-7187), Denis Jacob Machado (ORCiD: 0000-0001-9858-4515), Paula Prieto-Oliveira (ORCiD: 0000-0001-6999-3221), and Kary Ocaña (ORCiD: 0000-0002-2151-7418). All files use open, machine-readable formats (CSV, Markdown, plain text, FASTA, NEXUS, Python, Bash). Directory and file names contain no spaces or special characters. SupplementaryData1_Tables — Supplementary Tables See SupplementaryData1.tar.gz. Nine comma-separated value (CSV) files, one per supplementary table. SupplementaryTables.md describes the contents of each file. File Contents SupplementaryTables.md Brief description of each table and its columns. Table_S1.csv List of 6,906 DENV genomes retrieved from BV-BRC, including accession numbers and associated metadata (87 columns). Table_S2.csv Summary of software tools, versions, and parameter settings used in the analyses. Table_S3.csv Proportion of recombinants across clades and branch lengths from the phylogenetic tree. Table_S4.csv Taxa assigned to recombination events. Table_S5.csv Evolutionary models and parameter settings used to simulate alignments for RECOSIM performance evaluation. Table_S6.csv Distribution of recombinant DENV genomes per continent and country. Table_S7.csv Recombination events in DENV genomes detected both in this study and in previous published research. Table_S8.csv Evaluation of RECOSIM clustering strategies and parameter combinations. Table_S9.csv Comparison of RECOSIM and RDP5 detection performance. SupplementaryData2_Figures — Supplementary Figures See SupplementaryData2.tar.gz. A Markdown document with a contextual preamble and figure captions, together with eight PNG image files. Images are embedded in the Markdown and also available as standalone files. File Contents SupplementaryFigures.md Preamble describing the phylogenetic workflow and seven recombination case studies, followed by all figures with their captions. Figure_S1.png Conceptual workflow of the phylogenetic inference pipeline. Figure_S2.png SNP and similarity analysis for recombinant JQ922559 (DENV-4-I intra-genotypic event). Figure_S3.png SNP and similarity analysis for recombinant KX452048 (DENV-4-I intra-genotypic event). Figure_S4.png SNP and similarity analysis for recombinant MG560143 (DENV-2 inter-genotypic event). Figure_S5.png SNP and similarity analysis for recombinant KC964095 (DENV-2 inter-genotypic event). Figure_S6.png SNP and similarity analysis for recombinant KU517845 (DENV-2 inter-genotypic event). Figure_S7.png SNP and similarity analysis for recombinant JF295012 (DENV-3 inter-serotypic event). Figure_S8.png SNP and similarity analysis for recombinant ON123656 (DENV-1 inter-genotypic event). SupplementaryData3_Sequences — Sequence Data See SupplementaryData3.tar.gz. The multiple sequence alignment, genome partition scheme, and accession list for the DENV phylogenomic dataset. File Contents README.md Detailed description of each file in this directory. accessions.txt Plain-text list of 6,638 unique DENV genome accession IDs, one per line. alignment.fasta Multiple sequence alignment of DENV genomes in FASTA format, aligned against the FLAVi flavivirus reference framework. partitions.nexus Genome partition scheme in NEXUS format defining the boundaries of DENV genomic regions in FLAVi coordinates. tree.nwk Newick tree file of 6,642 unique flavivirus sequences generated with the phylogenetic inference pipeline. denv_zikv_wnv_alignment.fasta Multiple sequence alignment of DENV, ZIKV, and WNV genomes in FASTA format, aligned against the FLAVi flavivirus reference framework. SupplementaryData4_Scripts — Phylogenomic Analysis Scripts See SupplementaryData4.tar.gz. Python and Bash scripts supporting the phylogenomic analyses, with a Markdown methods description and a README. File Contents README.md Description of each script, including usage instructions and dependencies. PhylogenomicAnalyses.md Methods for the branch-length, phylogenetic placement, and tree topology analyses; includes accession IDs of the 192 sequences in the pruned DENV tree. ReproducePhylogenomicAnalyses.md Steps required to reproduce the phylogenomic analyses. Script_S1.py Phylogenetic inference pipeline integrating RAxML, TNT, and IQ-TREE2. Script_S2.py Extraction of recombinant proportions and branch lengths from phylogenetic trees. Script_S3.py Branch-length analysis: Mann–Whitney U test and Spearman rank correlation. Script_S4.py Clade-distance computation: smallest clade containing each recombinant and its parents. Script_S5.sh Visualisation of clade-size comparisons as a three-panel box-and-strip plot. Script_S6.sh Bash script generating TNT batch run files for the leave-one-out topology analysis. SupplementaryData5_Performance — RECOSIM Performance Evaluation See SupplementaryData5.tar.gz. File Contents performance.md Description of RECOSIM, the simulation design, evaluation protocol, and performance metrics (Hits ratio, Fails ratio, sensitivity, and precision).