Access automatic trees

Overview

CZ GEN EPI automatically generates an Overview tree that provides a broad overview of SARS-CoV-2 diversity. See the guide describing phylogenetic tree types for details regarding automatically generated trees. Here we describe how to access automatic tree builds on your account.

After reading this user guide, you will be able to: 

• Access SARS-CoV-2 automatic trees
• Understand why some automatic tree builds may fail

Accessing automatic trees

To access trees that are automatically generated by CZ GEN EPI:

1. Log in to your account and go to the SARS-CoV-2 Phylogenetic Tree page.
   
   CZ GEN EPI account page highlighting the Phylogenetic Trees tab
2. Look for the latest automatic build.
   
   Example Phylogenetic Tree page showing the latest automatic tree build. 
3. Click the "View tree in Nextstrain" icon to explore the interactive tree. See View trees in Nextstrain for details on how to visualize trees.
   
   

Failed automatic tree builds

It is rare for automatic tree builds to fail. By design, automatic trees provide an overview of virus diversity within the users' default location within the past three months and how it relates to other locations. Therefore, automatic tree builds will fail if there are no samples collected from the users’ default location within the past three months.  If this scenario does not apply to you and your automatic tree builds are failing, please contact our team by sending an email to hello@czgenepi.org.

If an automatic tree build fails, you will see a "FAILED" status flag by the tree name on the Phylogenetic Trees page.