Scripts for the analyses performed in the paper in a zipped folder.

BTV8analysis_gz.sh, BTV8analysis.sh, consensusfinal.R, consensusinitial.R, figure.R, finaldepthcorrection.R, namecorrection.R, and sequencecomparison.R are all used in the consensus sequence generation. Splits.R breaks fasta files into separate fasta files for codons 1, 2, and 3, the UTR, and regions of overlapping ORFs in segments 9 and 10. Reconstruction.R puts the reconstructed ancestor back together again. HockeyStickFInal.R, Map.R, MLTree.R, and BEASTTree.R all generate figures. ORF, open reading frame; UTR, untranslated region. (CPGZ)