CEIRR Risk Assessment Pipeline
Phylodynamics and computational modeling subgroup
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H5, H3, H1: Nextclade (GUI or command line)
H5, H7, and H9: LABEL (command line)
H5, H1, H3: BV-BRC subspecies classification (GUI)
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Parnas (Selects representative strains from tree in any dataset)
Pépinière (deduplicates and cleans up strains from GISAID and BV-BRC)
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phylo-rs - general use phylogenetics library
classLog - machine learning classification
Nextstrain - tutorials and documentation
splicer - sub-linear time phylogenetic placement
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UShER: rapidly places uploaded sequences into large trees to find most related sequences. Currently supports segment sequences for all Influenza A, and concatenated genomes for H5N1 outbreak genotypes B3.13 and D1.1
Curated UShER Taxonium trees:
a github repo of 432 UShER trees of viruses with RefSeq references and sufficient GenBank sequences, including 56 Influenza A trees -
TreeSort (command line)
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Curated H5N1 genetic changes inventory (downloadable spreadsheet)
Sequence Feature Variant Types (coming soon)
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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.