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Overview
You can access several types of phylogenetic tree builds on CZ GEN EPI, including automatically generated Overview trees and on-demand trees (Overview, Targeted, and Non-contextualized trees). See guides describing phylogenetic tree types and their sample composition for a detailed description of each tree. Below is a quick reference guide to distinguish phylogenetic tree types and their sample composition.
Tree types and their general features
Tree Type |
Source of samples on the tree |
Purpose |
Sample selection |
Note on user sample selection |
Automatic Overview trees |
Your jurisdiction and other regions |
Provide an overall picture of viral diversity within your jurisdiction, in the context of genetically similar samples from outside of your jurisdiction. |
No user-selected samples. Nextstrain will automatically select up to 2000 samples from your jurisdiction. |
No user sample selection |
On-demand Overview trees |
Your jurisdiction and other regions |
Summarize samples of interest from your jurisdiction, in the context of genetically similar samples from outside of your jurisdiction. |
Select samples from your jurisdiction that you want to force include on the tree. |
Less user-selection will give more room for samples to be automatically subsampled evenly across time. This will lead to a more unbiased overview. |
On-demand Targeted trees |
Your jurisdiction and other regions |
Outbreak investigation |
Select samples from a specific outbreak(s) of interest, or specific samples you would like to include on a tree (for example, to investigate how genomic data align with exposure history or interview data). |
Users should select less than a few hundred samples to minimize tree size. |
On-demand Non-contextualized trees |
Your jurisdiction |
Uncovering sampling bias in your own sampling effort |
Nextstrain will automatically include up to 2000 samples from your jurisdiction evenly sampled across time. You can opt to select samples of interest from your jurisdiction. |
Less user-selection will give more room for samples to be automatically subsampled evenly across time. This will lead to a more unbiased overview. |
Tree sample composition
Diagram summarizing sample composition for phylogenetic trees available on CZ GEN EPI.
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