Enhanced genome annotation strategy provides novel insights on the phylogeny of 'Flaviviridae': Supplementary material
- 1. University of North Carolina at Charlotte
- 2. University of California San Diego
Description
SUPPLEMENTARY MATERIAL
Index
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Table S1 (tableS1.csv): genomic data.
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Table S2 (tableS2.csv): character categorization for selected nodes.
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Table S3 (tableS3.csv): programs and parameters.
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Table S4 (tableS4.csv): annotation efficiency.
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File S1 (fileS1.gff): gene annotation.
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File S2 (fileS2.xml): configuration file for BEAST 2 (configuration.xml).
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Figure S1 (figureS1.pdf): dendrogram depicting the hierarchical clusters of trees based on match-split distances.
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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 there is a value below 90%). 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
FLAVi: an enhanced annotator for viral genomes of Flaviviridae.
Authors
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de Bernardi Schneider, Adriano. University of California San Diego. ORCID: 0000-0001-7487-266X.
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Jacob Machado, Denis. University of North Carolina at Charlotte. ORCID: 0000-0001-9858-4515. Corresponding author.
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Guirales, Sayal. University of North Carolina at Charlotte.
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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
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Corresponding author: Denis Jacob Machado, Ph.D.
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OrcID: 0000-0001-9858-4515.
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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.
Notes
Files
figureS1.pdf
Files
(4.1 MB)
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