Caily, clade-level phylo-trees at the country-level

Help and Getting Started
1

Hi - Complete newcomer to this GISAID interface, thank you for the helpful tutorials! I’m wondering if it is possible to:

  1. Retrieve daily phylo trees from multiple countries (i.e. country level aggregation)
  2. Instead of downloading the full tree each day, truncate the trees at the clade level, i.e. all the variants / genotypes within a specific clade are collapsed into the same clade.

Thanks for your suggestions!
Chris

2

Hi Chris

Retrieve daily phylo trees from multiple countries (i.e. country level aggregation)

You can see all the SARS-CoV-2 builds shared through nextstrain.org by a variety of researchers and public health groups here. I’m not aware of any groups generating daily country builds and sharing them through Nextstrain. We (Nextstrain) generate regional builds a couple of times per week, both for GISAID data and open (GenBank) data.

Instead of downloading the full tree each day, truncate the trees at the clade level, i.e. all the variants / genotypes within a specific clade are collapsed into the same clade.

This isn’t currently available, and variants aren’t always monophyletic!

3

Thanks James! Agreed on variants not being monophyletic, would just collapse to closest common ancestor, thanks for pointing that out.

Couldn’t open the link you pointed to with “public health groups here”.

4

Not sure why that link didn’t work! https://nextstrain.org/sars-cov-2/ is the page listing all the builds we know about, however we don’t keep track of how frequently they are updated. When you load each dataset, at the very bottom of the page it will tell you when the data was last updated (i.e. when the build was run).