University Library, University of Illinois at Urbana-Champaign
NEXUS file for Phylogeny and Biogeography of the Sharpshooters (Hemiptera: Cicadellidae: Cicadellinae)
Feng, Ling; Takiya, Daniela; Krishnankutty, Sindhu; Dietrich, Christopher; Zhang, Yalin (2023): NEXUS file for Phylogeny and Biogeography of the Sharpshooters (Hemiptera: Cicadellidae: Cicadellinae). University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-0855589_V1
The text file contains the original aligned DNA nucleotide sequence data used in the phylogenetic analyses of Feng et al. (in review), comprising the 3 protein-coding genes (histone H3, cytochrome oxidase I and 2) and 2 ribosomal genes (28S D8 and 16S). The text file is marked up according to the standard NEXUS format commonly used by various phylogenetic analysis software packages. The file will be parsed automatically by a variety of programs that recognize NEXUS as a standard bioinformatics file format. The first six lines of the file identify the file as NEXUS, indicate that the file contains data for 257 taxa (species) and 2995 characters (nucleotide positions), indicate that the characters are DNA sequence, that gaps inserted into the DNA sequence alignment are indicated by a dash, and that missing data are indicated by a question mark. The remainder of the file contains the aligned nucleotide sequence data for the five genes. Data partitions, representing the individual genes and different codon positions of the protein-coding genes, are indicated by the lines beginning "charset" near the end of the file. Two supplementary tables in the provided PDF file provide additional information on the species in the dataset, including the GenBank accession numbers for the sequence data (Table S1) and the DNA substitution models used for each of the data partitions used for analyses in the phylogenetic analysis program IQ-Tree (version 1.6.8) (Table S3), as described in the Methods section of the paper. The supplemental tables will also be linked to the article upon publication at the journal website.