Hi. My name is Jason and I teach undergraduate level Biology. I am interested in using NextStrain as an educational tool in my classroom by having my students access the data at the https://nextstrain.org/ncov website. I think the phylogeny tree is really great and I would love to have my students use it but I think its a little too complicated for them. I am looking for ways to simplify it what data is being shown. For example, there doesn’t seem to be a zoom in/out option like there is for the transmission map. Also, I think it would be great if I could filter the phylogeny tree by a location so that it ONLY shows the data for that location. Currently, when I filter by my home state, Georgia, the data lines are thicker but it is still really hard to make any sense of it because of all of the other lines. I appreciate any advice you could give.
Hi Jason – great to hear you’re thinking of using Nextstrain in this fashion. I know others have had success using it as a teaching tool
If you click on branches in the tree then the tree will zoom in to display only the clade deriving from that branch. You can zoom out in a stepwise fashion by clicking on the (new) root branch, or click “reset layout” (top right of the tree). If the branch you click on happens to have a label (as defined by the dataset itself) then this zoom-position will be saved in the URL so you can share it – for instance https://nextstrain.org/ncov/global?label=clade:20C will load zoomed in to SARS-CoV-2 clade “20C”.
Currently this isn’t possible unless you would like to generate a dataset yourself focusing only (or primarily) on Georgie samples – see this tutorial if you’re interested! Otherwise there may be a dataset listed here which is more targeted in terms of sampling, such as /ncov/north-america.
Hi James. Thank you so much for the quick and informative reply. This is really helpful!
Currently, when I filter by my home state, Georgia, the data lines are thicker but it is still really hard to make any sense of it because of all of the other lines.
We have some plans to make this work better here: https://github.com/nextstrain/auspice/issues/1132, but this is a little ways off.
Those changes would have a big impact, intuitive and useful. Sounds like the changes require a lot of work but I will keep an eye out for them.