Tools
UShER
UShER compares SARS-CoV2 sequences to find the most similar, complete, high-coverage samples from public databases (GISAID, NCBI, etc.).
Taxonium Viewer
The Taxonium Viewer uses UCSC’s SARS-CoV2 dataset and tools to display a phylogenetic tree. Investigators can quickly zoom into a sequence of interest and see its relations on the tree. A “subtree” does not have to be generated first as with NexStrain.
Big Tree Investigator
The PAUI Mapper offers SubmissionID/CaseID cross reference and visualization with local epidemiological data to visualize specimen sequences on the CDPH Dashboard.
CA Big Tree Cluster Tracker
The Cluster Tracker joins patient/case information to geographic data (such as addresses and maps) in a secure dashboard to facilitate contact tracing and surveillance. Integrates into known visualization and mapping tools (Google Maps, etc.)
Cluster Tracker is a prioritization and data exploration tool to help identify clusters of potential interest for further investigation.