Computational protocol: The First Outbreak of Eastern Equine Encephalitis in Vermont: Outbreak Description and Phylogenetic Relationships of the Virus Isolate

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Protocol publication

[…] Since there were no other sequences of EEEV from Vermont, studies were undertaken to determine genetic relationships with other strains from the US. Sequences were selected from GenBank () to represent isolates from diverse counties in multiple US states. Sequences for the E2 glycoprotein gene and the full coding sequences were aligned using MUSCLE on the Cipres Science Gateway [,]. Maximum likelihood inference was performed using RAxML 7.06 on the Cipres Science Gateway []. 1000 replicates of bootstrapping resampling were utilized to assess the accuracy of tree topologies. Output trees were generated for publication using FigTree v1.4. […]

Pipeline specifications

Software tools MUSCLE, CIPRES Science Gateway, RAxML, FigTree
Applications Phylogenetics, Nucleotide sequence alignment
Organisms Dromaius novaehollandiae
Diseases Encephalitis