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).
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/, aligns them to the RefSeq reference sequence for __STRAIN__ segment __SEGNUM__ (__SEGNAME__), __SEGREF__(https://www.ncbi.nlm.nih.gov/nuccore/__SEGREF__), using nextclade, and runs UShER to infer the tree structure and matOptimize to improve it under maximum parsimony.
In addition to metadata from GenBank and https://github.com/andersen-lab/avian-influenza (date, country, host, etc.), a "Differential selection in human vs. avian cells" phenotype score was calculated from Deep Mutational Scanning (DMS) experiments performed by the Bloom lab at the Fred Hutchinson Cancer Center (https://github.com/jbloomlab/PB2-DMS). The score displayed for each sequence was calculated by summing the per-mutation scores for all mutations found in that sequence, which are listed in the metadata as "Differential selection mutations".
The tree and metadata files can be downloaded from https://hgdownload.gi.ucsc.edu/hubs/__ASMDIR__/UShER___SEGREF__ .
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 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