Quick guide to phylogenetic tree types

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.