octoFLU: Automated Classification for the Evolutionary Origin of Influenza A Virus Gene Sequences Detected in U.S. Swine

The octoFLU classifier pipeline (A), PB2 and PB1 inferred maximum likelihood trees generated with 2 query strains, including the reference gene sequences (B), and example summary output generated for two contemporary U.S. swine influenza A genomes (C). The PB1 and PB2 gene tree examples demonstrate the genetic lineages of contemporary influenza A virus circulating in U.S. swine populations. The H1N1 pandemic 2009 (red) and LAIV genes (orange) are monophyletic clades nested within the TRIG lineage (purple); human seasonal (gray) and classical swine (blue) lineage genes are separate monophyletic clades. The query genes for A/swine/Nebraska/A02170137/2018 are labeled with a black star, and the query genes for A/swine/Oklahoma/A01785571/2018 are labeled by a black square. The trees are midpoint rooted for clarity, branch lengths are drawn to scale, and the scale bar indicates the number of nucleotide substitutions per site.