CEIRR Risk Assessment Pipeline
Phylodynamics and computational modeling subgroup
-
-
-
H5, H3, H1: Nextclade (GUI or command line)
H5, H7, and H9: LABEL (command line)
H5, H1, H3: BV-BRC subspecies classification (GUI)
-
Parnas (Selects representative strains from tree in any dataset)
Pépinière (deduplicates and cleans up strains from GISAID and BV-BRC)
-
phylo-rs - general use phylogenetics library
classLog - machine learning classification
Nextstrain - tutorials and documention
-
-
TreeSort (command line)
-
Curated H5N1 genetic changes inventory (downloadable spreadsheet)
Sequence Feature Variant Types (coming soon)
-
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.