The pandemic H1N1/09 virus (also called H1N1pdm) is a swine origin influenza A virus subtype H1N1 strain that was responsible for the 2009 swine flu pandemic. It is an ancestor of most H1N1 viruses now in circulation in humans.
We use the official nextclade dataset for sequence alignment and HA and NA clade assignment: nextstrain/flu/h1n1pdm (more specifically we use the CY121680.1 HA reference, the MW626056 Na reference and otherwise the references from the GCF_001343785.1 assembly).
Genspectrum uses all open influenza A data that is available on the INSDC (taxonid: 197911). To classify influenza segments and subtypes we use nextclade sort (using half of all k-mers for each subtype defined in https://github.com/anna-parker/InfluenzaAReferenceDB ) to improve classification). Where available we use the assembly information to group segments that are from the same sample/isolate. For all remaining segments we use a heuristic grouping algorithm to group all segments from the same sample/isolate using the metadata available from each segment.
For each individual influenza subtype you can view the CDS of each protein in the genome data viewer.