Cluster-Tracker

We apply a heuristic to the global public SARS-CoV-2 phylogenetic tree to identify groups of sequences from an area that may have recently migrated from outside the region. These may reflect cases of an infected traveler entering a region, followed by local spread. Many biases might affect these results including relative local sequencing effort, timeliness of data deposition into public sequence repositories, and accuracy of phylogenetic reconstruction. You can view each cluster in Theo Sanderson's taxonium and perform your own analysis with our toolkit and database.

Download full output file. Download the taxonium protobuf for viewing.

Please post an issue at the github or email me at jmcbroom@ucsc.edu if you have questions or feedback.