Enhanced genome annotation strategy provides novel insights on the phylogeny of 'Flaviviridae': Supplementary material

SUPPLEMENTARY MATERIAL Index Table S1 (tableS1.csv): genomic data. Table S2 (tableS2.csv): character categorization for selected nodes. Table S3 (tableS3.csv): programs and parameters. File S1 (fileS1.gff): gene annotation. File S2 (fileS2.xml): configuration file for BEAST 2 (configuration.xml). Figure S1 (figureS1.pdf): dendrogram depicting the hierarchical clusters of trees based on match-split distances. Figure S2 (figureS2.pdf): full version of the working phylogenetic hypothesis (tree No. 0 in table 1). Figure captions Figure S1: A dendrogram depicting the hierarchical clusters of trees based on match-split distances. Outgroup sequences (Hepacivirus, Pegivirus, and Pestivirus) were removed to guarantee the compared tree topologies would have the same terminals. Tree numbers correspond to those in table 1 of the manuscript. I. No outgroup sequences; some matrices were partitioned. II. Outgroup sequences and partitioned matrices. *This tree was produced without outgroup sequences. Figure S2: Full version of the working phylogenetic hypothesis (tree No. 0 in table 1). Branch lengths represent an estimation of the number of substitutions per site. Node labels indicate SH-aLRT support / ultrafast bootstrap (only shown if one of the values differs from 100/100). Clade names correlate to the character categorization analysis (see table S2). Branch labels represent the four genera: I = Pestivirus; II = Pegivirus; III = Hepacivirus; IV = Flavivirus. * The Ecuador Paraiso Escondido virus (EPEV) was isolated from sand flies (Psathyromyia abonnenci). The EPEV was the first sand fly-borne Flavivirus identified in the New World. Manuscript title Enhanced genome annotation strategy provides novel insights on the phylogeny of Flaviviridae. Authors de Bernardi Schneider, Adriano. University of California San Diego. ORCID: 0000-0001-7487-266X. Jacob Machado, Denis. University of North Carolina at Charlotte. ORCID: 0000-0001-9858-4515. Corresponding author. Janies, Daniel. University of North Carolina at Charlotte. First author: Adriano de Bernardi Schneider and Denis Jacob Machado have contributed equally to the manuscript. Contact information Corresponding author: Denis Jacob Machado, Ph.D. OrcID: 0000-0001-9858-4515. Email: dmachado [at] uncc.edu. Other additional material In addition to the material listed above, all 31 tree topologies and 15 alignment matrices discussed in this manuscript will are available in TreeBASE (http://purl.org/phylo/treebase/phylows/study/TB2:S24096) after the publication of the manuscript. The FLAVi pipeline and all the original scripts are available at GitLab (https://gitlab.com/MachadoDJ/FLAVi). The web application can be accessed at http://flavi-web.com.