About Taxonium

Taxonium is a web application for exploring phylogenetic trees. Find out more at the Github repository (https://github.com/theosanderson/taxonium) or read the documentation (https://docs.taxonium.org).

About the tree

This tree was constructed by the Pathogen Genomics Group at the University of California Santa Cruz (UCSC) Genomics Institute. Our automated pipeline downloads Influenza A sequences from GenBank (i.e. the INSDC databases) and SRA assemblies from https://github.com/andersen-lab/avian-influenza/, identifies isolates that belong to the H5N1 clade 2.3.4.4b genotype D1.1 branches of per-segment trees, concatenates the segments of each isolate in largest to smallest order (PB2, PB1, PA, HA, NP, NA, MP, NS), aligns the concatenated sequences to a concatenated reference (PQ664446.1, PQ798039.1, PQ859340.1, PQ663857.1, PQ585621.1, PQ664459.1, PQ663860.1, PQ797957.1), using nextclade, and runs UShER to infer the tree structure and matOptimize to improve it under maximum parsimony.

About the metadata

In addition to metadata from GenBank and https://github.com/andersen-lab/avian-influenza (date, country, host, etc.), five HA phenotype scores were calculated from Deep Mutational Scanning (DMS) experiments performed by the Bloom lab at the Fred Hutchinson Cancer Center (https://dms-vep.org/Flu_H5_American-Wigeon_South-Carolina_2021-H5N1_DMS/):

as well as one PB2 phenotype: Differential selection in human vs. avian cells. The scores displayed for each sequence were calculated by summing the per-mutation scores for all mutations found in that sequence.

Downloads

The tree and metadata files can be downloaded from https://hgdownload.gi.ucsc.edu/hubs/__ASMDIR__/UShER___SEGREF__ .

Citations

If you use Taxonium in your research, please cite:
Theo Sanderson (2022) Taxonium, a web-based tool for exploring large phylogenetic trees eLife 11:e82392.
https://doi.org/10.7554/eLife.82392

If you use the tree in your research, please cite:
Jakob McBroome et al. (2021) A Daily-Updated Database and Tools for Comprehensive SARS-CoV-2 Mutation-Annotated Trees Mol Biol Evol 38(12):5819-5824.
https://doi.org/10.1093/molbev/msab264

If you use the Deep Mutational Scanning HA phenotype scores in your research, please cite:
Bernadeta Dadonaite et al. (2024) Deep mutational scanning of H5 hemagglutinin to inform influenza virus surveillance
https://doi.org/10.1371/journal.pbio.3002916

If you use the Deep Mutational Scanning PB2 phenotype scores in your research, please cite:
Shirleen YQ Soh et al. (2019) Comprehensive mapping of adaptation of the avian influenza polymerase protein PB2 to humans eLife 8:e45079.
https://doi.org/10.7554/eLife.45079