CEIRR Risk Assessment Pipeline

Phylodynamics and computational modeling subgroup

GenBank (all influenza A)
GenBank (H5Nx)
BV-BRC (H5N1 2024)
Andersen lab H5N1 cattle outbreak
SRA (H5N1)
GISAID
H5N1: GenoFlu
Swine: OctoFlu
H5: Nextclade (GUI or command line)
H5, H7, and H9: LABEL (command line)
H5: BV-BRC subspecies classification (GUI)
Parnas (Selects representative strains from tree in any dataset)
Tardis
Smot
SAMPI

UShER
H5Nx
TreeSort (command line)
FluMut
HA numbering tool
FluServer
FluTile
Sequence Feature Variant Types (coming soon)
Livestock estimation
Movebank
Comtrade
BirdFlow
eBird

This page is maintained by the CEIRR RAP Phylodynamics and Computational Modeling subgroup. For information or suggestions, please contact the subgroup leaders, Martha Nelson and Louise Moncla.