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The Nextstrain website
https://nextstrain.org
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adding in time resolution for avian influenza builds to allow 2y and … #837

Closed lmoncla closed 2 months ago

lmoncla commented 2 months ago

…all-time builds for h5nx and h5n1, and all-time builds only for h9n2 and h7n9

Description of proposed changes

We recently made a series of updates to the avian-flu builds to provide a more in-depth view of the ongoing H5Nx outbreak of 2.3.4.4b viruses. We now have 2 different time resolutions for H5Nx and H5N1: 2y and all-time. This pull request updates manifest_core.json to reflect these changes.

trvrb commented 2 months ago

@lmoncla: Can we update default from h5nx to h5n1? It seems like this is more expected by the community and the vast majority of recent H5 viruses are H5N1 viruses. And all the viruses we care about in the recent 2.3.4.4b outbreak are H5N1.

Otherwise this looks good to merge now for me.

lmoncla commented 2 months ago

@trvrb now that we've switched over to the 2y build as default, switching back to h5n1 as default is fine by me. The all-time h5n1 tree gives a very incomplete picture of h5 evolution because it is missing a long stretch of time during which the ancestral 2.3.4.4 H5 HA was reassorting with other NAs. But I think that given these updates, fine to revert to H5N1 as default.

trvrb commented 2 months ago

Thank you @lmoncla! I imagine these defaults to be something that we can update frequently as situation changes. I like H5N1 / 2y as default given that this is probably the best place to take someone who clicks on the "avian flu" tile because they're interested in what's going on.