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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 |
Purpose |
User inputs (see how to select samples) |
Samples on the tree |
|
Automatic Overview trees |
Provide an overall picture of viral diversity within your area, in the context of genetically similar samples from outside of your location. |
No user inputs. Nextstrain will automatically select up to 2000 samples from your default location (sampled across time) and add closely-related contextual samples. |
Automatically selected samples from your default location, closely-related contextual samples, and randomly-selected samples |
|
On-demand Overview trees |
Summarize samples of interest based on location, lineage(s), and collection date, in the context of genetically similar samples from outside of your location. |
You can define samples based on location, lineage, and/or collection date range of interest. You can also select additional samples outside the defined parameters using sample IDs. |
User-defined and user-selected samples in addition to automatically selected samples, including closely-related contextual samples and randomly-selected samples |
|
On-demand Targeted trees |
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). |
User-selected samples in addition to automatically selected samples, including closely-related contextual samples and randomly-selected samples |
|
On-demand Non-contextualized trees |
Uncovering sampling bias in your own sampling effort |
You can define samples based on location, lineage, and collection date range of interest. You can also select additional samples outside the defined parameters using sample IDs. |
User-defined and user-selected samples with NO contextual or random samples. |
Tree sample composition
Diagram summarizing sample composition for phylogenetic trees available on CZ GEN EPI. Samples include samples of interest (i.e., user-defined and user-selected samples) and samples automatically selected by Nextstrain. To view the distribution of each sample type in tree builds see Understanding on-demand tree sample composition.
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