Get familiar with Phylogenetic Tree page

Overview

The Phylogenetic Tree page is your “home base” for managing all of your trees within a pathogen workspace. This page shows all of the automatic trees and on-demand trees that you and other members of your group have built through CZ GEN EPI. Below are details regarding functionalities within the Phylogenetic Tree page.

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

• Navigate around the the Phylogenetic Tree page
• Use all of the functionality available on the Phylogenetic Tree page

Keep Tract of Your Trees

The Phylogenetic Tree page provides general information about how many trees have been built, their completion status (started, completed, or failed), when they were created, and tree type. To get to the Phylogenetic Tree page, click on the Phylogenetic Trees tab at the top of the Sample page for a given pathogen.

Example SARS-CoV-2 Phylogenetic Tree page highlighting number of trees, status, date and type.

Example SARS-CoV-2 Phylogenetic Tree page showing how automatic and on-demand tree builds are distinguished under the tree names. On-demand trees will specify the name or the email address of the user who built the tree.

Check on the status of your tree after creating a given tree build. You will see one of the following status by your tree build name: 

• Started: Tree building has started. It takes 8-12 hours to complete a tree build.
• Completed: Tree building completed. Completed trees can be viewed in Nextstrain, downloaded, and/or deleted (see below). 
• Failed: Tree build was not completed due to an error (failed). Non-contextualized tree builds will fail if samples from selected lineage(s) and/or date range do not exist in CZ GEN EPI or GISAID. Please contact support (hello@czgenepi.org) if this sample selection scenario does not apply to your build and your tree still fails to complete. 

Searching & Filtering Trees

You can search for specific trees within the Phylogenetic Tree page by tree name, creation date, and/or tree type. 

Use the search box to find tree builds of interest.

Example of tree search using the term "Overview" (tree type). Note that this search effectively filters trees on the table and only Overview trees are shown.

Managing Your Trees

After a given tree build has been completed, you can view it in Nextstrain, interpret it using Galago, download it, edit its name, or delete it using the menu icons on the right of the tree table.

Menu icons to manage trees after they have been completed.

Viewing trees

To view trees, click on the "View in Nextstrain" icon . You will be redirected to Nextstrain to view and explore your tree using an interactive visualization program.

• See Viewing trees in Nextstrain for details.

Downloading trees

You have the option to download three types of tree files. To download tree files, click on the download icon and select the file type of interest, including:

• • An interactive tree file format (‘.json’ file extension) containing Private IDs
  • An interactive tree file format (‘.json’ file extension) containing Public IDs.
  • A tab-delimited file listing samples on the tree using their Public or Private IDs.

Download icon and dropdown menu 

Editing tree names

You can easily change the title or name of your trees. To do this:

1. Click on "Edit Tree Name" under the More Actions dropdown menu.More Actions icon and dropdown menu. Click on "Edit Tree Name" to change the name.
2. A dialog box will appear where you can specify and update a given tree name. Note the following when specifying a new name:

• Do not include personally identifiable information (PII) on the tree name.
• Names cannot exceed 128 characters.

Dialog box for editing tree names. Click "Update" to save the changes.

Deleting trees 

You can delete tree builds that are no longer needed. To do this:

1. Click on "Delete Tree" under the More Actions dropdown menu.More Actions icon and dropdown menu. Click on "Delete Tree" to remove the tree from your CZ GEN EPI account.
2. You will be prompted to confirm the delete action. Click "Delete" to remove the tree from your CZ GEN EPI account. Note that this action cannot be undone.

Example pop-up box prompting user to confirm and complete tree build deletion.